Run 3Dtex-bagg
# 1) From 100% dataset, Create train/validation (80%) / heldout (20%) partitions
sqlite <- dbDriver("SQLite")
conn <- dbConnect(sqlite, "textureUpdatedFeatures.db")
# 2) all T1w features
lesionsQuery <- dbGetQuery(conn, "SELECT *
FROM stage1features
INNER JOIN lesion ON (stage1features.lesion_id = lesion.lesion_id)
INNER JOIN f_T2 ON (stage1features.lesion_id = f_T2.lesion_id)")
# For bootstrap resampling, createResample is used
# Randomization is done at the patient level, so that bootstrapping preserves lesion independence
lesionsQuery = subset(lesionsQuery, lesion_label != "fociB" & lesion_label != "fociM" ) # exclude foci at this point
id_cad_pts = lesionsQuery$cad_pt_no_txt
uniq_cad = unique(lesionsQuery$cad_pt_no_txt)
npatients = 1:length(uniq_cad)
# when y is a factor in an attempt to balance the class distributions within the splits.
# The names of the list objects will denote the fold membership using the pattern
# resamples." meaning the ith section (of k) of the jth cross-validation set (of times).
set.seed(1234)
npatients = length(uniq_cad)
kfcvpartitionsetD <- createFolds(y = 1:length(uniq_cad),## the outcome data are needed
k = 10,
list = TRUE)
## using 3Dtexture first + Boosting
perf_imgT2 = data.frame();
perf_allT2 = data.frame();
perf_imgT1 = data.frame();
perf_all = data.frame();
## holders for reature rankings
imgT2featsel = data.frame()
allT2featsel = data.frame()
imgT1featsel = data.frame()
allfeatsel = data.frame()
cvauc_imgT2 = c()
cvauc_allT2 = c()
cvauc_imgT1 = c()
cvauc_all = c()
# perform k-fold-out
for(k in 1:10){ # 1:10f cv
## Create folds leave-one-patient-out
allfT2 = read3Dtex_T2uniqcad_parti(id_cad_pts, uniq_cad, kfcvpartitionsetD, 10, k)
allfT1 = read3Dtex_T1uniqcad_parti(id_cad_pts, uniq_cad, kfcvpartitionsetD, 10, k)
allfT1T2 = read3Dtex_T1T2uniqcad_parti(id_cad_pts, uniq_cad, kfcvpartitionsetD, 10, k)
## formant
T2train = allfT2[[1]]; T2traininfo = allfT2[[5]]; T2trainids = T2traininfo$lesion_id;
T2test = allfT2[[2]]; T2testinfo = allfT2[[6]]; T2testids = T2testinfo$lesion_id;
T1train = allfT1[[1]]; T1traininfo = allfT1[[5]]; T1trainids = T1traininfo$lesion_id;
T1test = allfT1[[2]]; T1testinfo = allfT1[[6]]; T1testids = T1testinfo$lesion_id;
T1T2train = allfT1T2[[1]]; T1T2traininfo = allfT1T2[[5]]; T1T2trainids = T1T2traininfo$lesion_id;
T1T2test = allfT1T2[[2]]; T1T2testinfo = allfT1T2[[6]]; T1T2testids = T1T2testinfo$lesion_id;
# remove radiologist based BIRADS category and measured muscle-to-lesion SI
# add predicted T2w features
T2LMSIR = getid_predLMSIR(LMSIR_lop, T2trainids)
T2wSI = getid_predT2wSI(perfT2wSI_lop, T2trainids)
imgT2train = T2train[,-c(2,5,ncol(T2train))] # exlude orig_label
wpredT2train = cbind(T2train[,-c(ncol(T2train))], LMSIR_predicted=T2LMSIR$LMSIR_predicted, T2wSI_predicted=T2wSI$T2wSI_predicted)
wpredT2train$find_t2_signal_int = as.factor(wpredT2train$find_t2_signal_int)
wpredT2train$T2wSI_predicted = as.factor(wpredT2train$T2wSI_predicted)
T1train = T1train[,-c(ncol(T1train))]
# remove radiologist based BIRADS category and measured muscle-to-lesion SI
# add predicted T2w features
T1T2LMSIR = getid_predLMSIR(LMSIR_lop, T1T2trainids)
T1T2wSI = getid_predT2wSI(perfT2wSI_lop, T1T2trainids)
########## consider differneces
imgT1T2train = T1T2train[,-c(ncol(T1T2train))]
imgT1T2train$find_t2_signal_int = as.factor(imgT1T2train$find_t2_signal_int)
wpredT1T2train = cbind(imgT1T2train, LMSIR_predicted=T1T2LMSIR$LMSIR_predicted, T2wSI_predicted=T1T2wSI$T2wSI_predicted)
wpredT1T2train$T2wSI_predicted = as.factor(wpredT1T2train$T2wSI_predicted)
# with datasets: T2train, wpredT2train, T1train, T1T2train, wpredT1T2train
selrrfimgT2 = RRF_featsel(imgT2train, "imgT2")
selrrfallT2 = RRF_featsel(wpredT2train, "allT2")
selrrfimgT1 = RRF_featsel(T1train, "imgT1")
selrrfall = RRF_featsel(wpredT1T2train, "all")
## group with all of the features spaces combined, most contributing T2w feature
imgT2featsel = rbind(imgT2featsel, cbind(selrrfimgT2, kfcv=k) )
allT2featsel = rbind(allT2featsel, cbind(selrrfallT2, kfcv=k) )
imgT1featsel = rbind(imgT1featsel, cbind(selrrfimgT1, kfcv=k) )
allfeatsel = rbind(allfeatsel, cbind(selrrfall, kfcv=k) )
##################
# Define datasets
##################
# define datasets: imgT2wfeatures allT2wfeatures, imgT1wfeatures, allfeatures
imgT2features = imgT2train[,c("lesion_label", selrrfimgT2$selfeat)]
allT2features = wpredT2train[,c("lesion_label",selrrfallT2$selfeat)]
imgT1features = T1train[,c("lesion_label",selrrfimgT1$selfeat)]
allfeatures = wpredT1T2train[, c("lesion_label",selrrfall$selfeat)]
##################
# Get Test info data
##################
dfinfo = cbind(T2testinfo[,c(1,3,6,24:26)],
find_t2_signal_int=T2test$find_t2_signal_int)
print(dfinfo)
## apend LMSIR and T2wSI in case is used by classifier
testLMSIR = getid_predLMSIR(LMSIR_lop, T2testids)
testT2wSI = getid_predT2wSI(perfT2wSI_lop, T2testids)
T2test = cbind(T2test, LMSIR_predicted=testLMSIR$LMSIR_predicted,
T2wSI_predicted=testT2wSI$T2wSI_predicted)
## for T1T2
## apend LMSIR and T2wSI in case is used by classifier
testLMSIR = getid_predLMSIR(LMSIR_lop, T1T2testids)
testT2wSI = getid_predT2wSI(perfT2wSI_lop, T1T2testids)
T1T2test = cbind(T1T2test, LMSIR_predicted=testLMSIR$LMSIR_predicted, T2wSI_predicted=testT2wSI$T2wSI_predicted)
##################
# Build final classifiers
##################
# data = imgT2features,
cat("\n============ bagging trees treedata_imgT2 \n")
# train trees
treedata_imgT2 <- NH_looforestTrain(imgT2features, T2test)
#treedata_imgT2 = adjustweights_NH(treedata_imgT2$forest, imgT2features, T2test)
######## data = allT2features,
cat("\n============ bagging trees treedata_allT2 \n")
# train trees
treedata_allT2 <- NH_looforestTrain(allT2features, T2test)
#treedata_allT2 = adjustweights_NH(treedata_allT2$forest, allT2features, T2test)
####### data = imgT1features,
cat("\n============ bagging trees treedata_imgT1 \n")
# train trees
treedata_imgT1 <- NH_looforestTrain(imgT1features, T1test)
#treedata_imgT1 = adjustweights_NH(treedata_imgT1$forest, imgT1features, T1test)
####### data = allfeatures,
cat("\n============ bagging trees treedata_all \n")
# train trees
treedata_all <- NH_looforestTrain(allfeatures, T1T2test)
#treedata_all = adjustweights_NH(treedata_all$forest, allfeatures, T1T2test)
##################
### predict for each classifier
##################
## for treedata_imgT2
rules = data.frame(C=treedata_imgT2$testperf$testpred_NH, NC=1-treedata_imgT2$testperf$testpred_NH)
rules$pred = apply(rules, 1, which.max)
perfcv_imgT2 = data.frame(id=T2testinfo$lesion_id,
C=treedata_imgT2$testperf$testpred_NH,
NC=1-treedata_imgT2$testperf$testpred_NH,
pred=ifelse(rules$pred==1,"C","NC"), obs=T2test$lesion_label)
auc_imgT2 = roc(perfcv_imgT2$obs, perfcv_imgT2$C)
perf_imgT2 = rbind(perf_imgT2, cbind(dfinfo,perfcv_imgT2) )
print(head(perfcv_imgT2))
cvauc_imgT2 = c(cvauc_imgT2, auc_imgT2$auc)
# for treedata_allT2
rules = data.frame(C=treedata_allT2$testperf$testpred_NH, NC=1-treedata_allT2$testperf$testpred_NH)
rules$pred = apply(rules, 1, which.max)
perfcv_allT2 = data.frame(id=T2testinfo$lesion_id,
C=treedata_allT2$testperf$testpred_NH,
NC=1-treedata_allT2$testperf$testpred_NH,
pred=ifelse(rules$pred==1,"C","NC"), obs=T2test$lesion_label)
auc_allT2 = roc(perfcv_allT2$obs, perfcv_allT2$C)
perf_allT2 = rbind(perf_allT2, cbind(dfinfo,perfcv_allT2) )
print(head(perfcv_allT2))
cvauc_allT2 = c(cvauc_allT2, auc_allT2$auc)
## for treedata_imgT1
rules = data.frame(C=treedata_imgT1$testperf$testpred_NH, NC=1-treedata_imgT1$testperf$testpred_NH)
rules$pred = apply(rules, 1, which.max)
perfcv_imgT1 = data.frame(id=T1testinfo$lesion_id,
C=treedata_imgT1$testperf$testpred_NH,
NC=1-treedata_imgT1$testperf$testpred_NH,
pred=ifelse(rules$pred==1,"C","NC"), obs=T1test$lesion_label)
auc_imgT1 = roc(perfcv_imgT1$obs, perfcv_imgT1$C)
perf_imgT1 = rbind(perf_imgT1, cbind(dfinfo,perfcv_imgT1) )
print(head(perfcv_imgT1))
cvauc_imgT1 = c(cvauc_imgT1, auc_imgT1$auc)
# for treedata_all
rules = data.frame(C=treedata_all$testperf$testpred_NH, NC=1-treedata_all$testperf$testpred_NH)
rules$pred = apply(rules, 1, which.max)
perfcv_all = data.frame(id=T1T2testinfo$lesion_id,
C=treedata_all$testperf$testpred_NH,
NC=1-treedata_all$testperf$testpred_NH,
pred=ifelse(rules$pred==1,"C","NC"), obs=T1T2test$lesion_label)
auc_all = roc(perfcv_all$obs, perfcv_all$C)
perf_all = rbind(perf_all, cbind(dfinfo,perfcv_all) )
print(head(perfcv_all))
cvauc_all = c(cvauc_all, auc_all$auc)
# AUC
rocperf_imgT2 = roc(perf_imgT2$obs, perf_imgT2$C)
print(rocperf_imgT2)
rocperf_allT2 = roc(perf_allT2$obs, perf_allT2$C)
print(rocperf_allT2)
rocperf_imgT1 = roc(perf_imgT1$obs, perf_imgT1$C)
print(rocperf_imgT1)
rocperf_all = roc(perf_all$obs, perf_all$C)
print(rocperf_all)
# plot every 10 patients
## plot ROCs each pass individually in l-o-p heldout test cases
par(mfrow=c(1,1))
n=15
colors = rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, alpha = 1)
# plot 1/4
p1 = calcAUC_plot(perf_imgT2$obs, perf_imgT2$C,
xptext=0.45, yptext=0.75 ,colors[2], atitle="")
par(new=TRUE)
p2 = calcAUC_plot(perf_allT2$obs, perf_allT2$C,
xptext=0.55, yptext=0.65 ,colors[9], atitle="")
par(new=TRUE)
p3 = calcAUC_plot(perf_imgT1$obs, perf_imgT1$C,
xptext=0.65, yptext=0.55 ,colors[11], atitle="")
par(new=TRUE)
p4 = calcAUC_plot(perf_all$obs, perf_all$C,
xptext=0.75, yptext=0.45 ,colors[14],
atitle=paste0("ROCs 10f-patient out cv test k-fold= ",k))
legend("bottomright",
legend = c(paste0("imgT2w"),
paste0("imgT2w+predT2w"),
paste0("imgT1w"),
paste0("imgT1+imgT2w+predT2w")),
col = c(colors[2],colors[9],colors[11],colors[14]), lwd = 2)
# save current state k patient out
save.image(paste0("Outputs/NH_addeddiagvalue_3Dtexbagg_cv",k,".RData"))
}
## massB massM nonmassB nonmassM
## 217 152 131 67
## massB massM nonmassB nonmassM
## 25 14 11 10
## massB massM nonmassB nonmassM
## 217 152 131 67
## massB massM nonmassB nonmassM
## 25 14 11 10
## massB massM nonmassB nonmassM
## 217 152 131 67
## massB massM nonmassB nonmassM
## 25 14 11 10
## RRF 1.6
## Type rrfNews() to see new features/changes/bug fixes.
##
## Attaching package: 'RRF'
##
## The following object is masked from 'package:ranger':
##
## importance
##
## The following object is masked from 'package:ggplot2':
##
## margin
## 0.07906977 0.05
## -0.005050505 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2RGH_var" "T2texture_correlation_nondir" "T2RGH_mean" "ave_T210"
## [5] "T2texture_energy_nondir" "T2texture_inversediffmoment_nondir" "ave_T211" "T2skew_F_r_i"
## [9] "T2grad_margin_var" "T2texture_entropy_nondir" "T2var_F_r_i" "ave_T217"
## [13] "T2texture_sumaverage_nondir" "ave_T28" "ave_T21" "T2texture_contrast_nondir"
## [17] "ave_T213" "ave_T219" "T2_lesionSI" "ave_T26"
## [21] "ave_T214" "T2max_F_r_i" "T2min_F_r_i" "ave_T216"
## [25] "ave_T218" "ave_T29" "ave_T25" "T2texture_sumentropy_nondir"
## [29] "T2texture_sumvariance_nondir" "T2kurt_F_r_i" "ave_T23" "ave_T215"
## [33] "ave_T22" "ave_T24" "ave_T20" "T2_lesionSIstd"
## -0.03645833 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_var" "T2texture_entropy_nondir" "ave_T210" "T2grad_margin_var" "LMSIR"
## [6] "T2texture_diffvariance_nondir" "ave_T27" "ave_T21" "LMSIR_predicted" "T2_lesionSIstd"
## [11] "ave_T213" "ave_T25" "ave_T217" "ave_T26" "ave_T214"
## [16] "ave_T211" "T2texture_sumaverage_nondir" "T2_lesionSI" "T2min_F_r_i" "T2texture_correlation_nondir"
## [21] "ave_T23" "ave_T22" "ave_T24" "ave_T20" "T2kurt_F_r_i"
## [26] "ave_T216" "T2wSI_predicted" "find_t2_signal_int"
## 0.07189542 0.05
## -0.05633803 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "texture_variance_nondir_post2" "SER_countor" "texture_diffvariance_nondir_post1"
## [4] "V1" "texture_inversediffmoment_nondir_post4" "V4"
## [7] "V2" "var_F_r_i" "Kpeak_inside"
## [10] "Vr_increasingRate_countor" "Vr_decreasingRate_inside" "Slope_ini_inside"
## [13] "kurt_F_r_i" "texture_diffvariance_nondir_post2" "dce2SE0"
## [16] "edge_sharp_std" "texture_contrast_nondir_post3" "dce2SE11"
## [19] "dce3SE18" "maxVr_countor" "earlySE5"
## [22] "dce2SE17" "dce3SE17" "earlySE2"
## [25] "earlySE18" "UptakeRate_inside" "dce2SE15"
## [28] "earlySE16" "lateSE5" "texture_entropy_nondir_post1"
## [31] "ivVariance" "A_countor" "dce3SE13"
## [34] "earlySE9" "skew_F_r_i" "edge_sharp_mean"
## [37] "dce3SE11" "A_inside"
## 0.1176471 0.05
## 0.04 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "texture_variance_nondir_post1" "SER_inside" "V11"
## [4] "texture_inversediffmoment_nondir_post2" "V12" "V8"
## [7] "min_F_r_i" "T2kurt_F_r_i" "var_F_r_i"
## [10] "V14" "Tpeak_countor" "texture_correlation_nondir_post1"
## [13] "texture_sumentropy_nondir_post4" "T2RGH_mean" "texture_sumaverage_nondir_post3"
## [16] "Vr_decreasingRate_inside" "dce2SE14" "dce2SE15"
## [19] "ave_T212" "lateSE1" "ave_T26"
## [22] "lateSE16" "edge_sharp_mean" "T2grad_margin_var"
## [25] "Vr_decreasingRate_countor" "lateSE7" "dce2SE5"
## [28] "ivVariance" "alpha_countor" "V6"
## [31] "texture_energy_nondir_post1" "T2max_F_r_i" "ave_T218"
## [34] "texture_diffvariance_nondir_post1" "T2texture_energy_nondir" "k_Max_Margin_Grad"
## [37] "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 1 1 0002 6745896 4 nonmassM InsituDuctal None
## 32 32 0173 5123923 4 nonmassB DUCT PAPILLOMA None
## 40 40 0190 6760690 4 massM InvasiveDuctal None
## 41 41 0190 6760690 4 nonmassM InvasiveDuctal None
## 51 51 0205 5085133 4 massB FIBROEPITHELIAL Hyperintense
## 103 103 0553 6687000 2 massB BENIGN BREAST TISSUE Hyperintense
## 104 104 0561 4668611 4 massB FIBROADENOMA Hypointense or not seen
## 116 116 0606 6781309 4 massB ATYPICAL DUCTAL HYPERPLASIA Hyperintense
## 117 117 0608 5094101 4 massB BENIGN BREAST TISSUE Hyperintense
## 134 134 0672 4899757 5 nonmassM InsituDuctal None
## 152 152 0696 6983274 4 massB BENIGN BREAST TISSUE Hypointense or not seen
## 153 153 0700 4660805 5 massM InvasiveDuctal None
## 165 165 0718 4962581 4 massB FIBROCYSTIC None
## 179 179 0730 5009497 5 massM InvasiveDuctal None
## 185 185 0740 4842984 4 nonmassB SCLEROSING INTRADUCTAL PAPILLOMA Slightly hyperintense
## 216 216 0779 4934249 5 massB SCLEROSING ADENOSIS None
## 217 217 0779 4934249 5 massM InvasiveDuctal None
## 227 227 0796 860773 4 nonmassB ATYPICAL LOBULAR HYPERPLASIA None
## 228 228 0799 5372294 4 massB FIBROCYSTIC Slightly hyperintense
## 229 229 0802 4600874 4 massM InvasiveDuctal None
## 232 232 0807 5235491 5 nonmassM InsituDuctal None
## 284 284 0871 5130094 4 massM InvasiveLobular None
## 285 285 0871 5130094 4 massM InsituDuctal None
## 286 286 0871 5130094 4 massM InvasiveLobular None
## 301 301 0885 6747175 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 309 309 0918 6976567 4 massB FIBROADENOMA Hyperintense
## 332 332 0993 6979299 4 massB PHYLLODES TUMOR Hyperintense
## 367 367 1086 7173349 6 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 378 378 2016 7052211 4 massB FIBROADENOMA Hyperintense
## 380 380 2023 5141524 6 massM InvasiveDuctal None
## 399 399 2059 7749617 4 nonmassB COLUMNAR CELL CHANGES None
## 413 413 3005 4974097 3 nonmassB BENIGN BREAST TISSUE None
## 414 414 3005 6757337 3 nonmassM InsituDuctal Hypointense or not seen
## 415 415 3005 5057668 2 nonmassB FIBROCYSTIC None
## 416 416 3005 6757337 4 nonmassM InsituDuctal Hypointense or not seen
## 422 422 3020 7395195 4 massB STROMAL HYPERPLASIA Hypointense or not seen
## 424 424 3023 7106703 6 massM InvasiveDuctal None
## 451 451 3065 7037223 4 massB ADENOSIS Hypointense or not seen
## 452 452 3065 7037223 4 massB ADENOSIS Hypointense or not seen
## 453 453 3070 7085188 4 massB DUCTAL HYPERPLASIA WITHOUT ATYPIA Hypointense or not seen
## 465 465 3081 7041435 5 nonmassB COLUMNAR CELL CHANGES Hypointense or not seen
## 466 466 3081 7041435 5 nonmassM InsituDuctal Hypointense or not seen
## 476 476 4003 7056445 4 nonmassB FLORID DUCTAL HYPERPLASIA None
## 477 477 4003 7056445 4 nonmassB FLORID DUCTAL HYPERPLASIA None
## 492 492 4029 7633460 4 massB InsituLobular None
## 493 493 4029 7633460 4 massB InsituLobular None
## 503 503 4047 7009608 4 massB FIBROCYSTIC Hypointense or not seen
## 514 514 6015 5082265 6 massM InvasiveDuctal None
## 515 515 6015 5082265 6 nonmassM InvasiveDuctal None
## 518 518 6018 5088825 5 nonmassM InvasiveLobular None
## 521 521 6021 4798692 4 massB ATYPICAL LOBULAR HYPERPLASIA None
## 534 534 6029 5083338 6 massB FIBROADENOMA Hypointense or not seen
## 535 535 6029 5083338 6 massB FIBROADENOMA Hypointense or not seen
## 536 536 6029 6772981 4 massB FIBROADENOMA Hypointense or not seen
## 538 538 6034 4997881 6 massM InvasiveDuctal Hyperintense
## 539 539 6034 4997881 6 massM InvasiveDuctal Hyperintense
## 540 540 6034 4997881 6 nonmassM InvasiveDuctal None
## 593 593 7008 6875110 6 massM InvasiveLobular Hyperintense
## 602 602 7045 6760802 4 massB BENIGN BREAST TISSUE Hypointense or not seen
## 631 631 7190 7013378 3 massB COLUMNAR CELL CHANGES Hyperintense
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6699667 0.6290509
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7600706 0.6475694
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.7941007 0.5850694
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.868892 0.4895833
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6699667 0.6290509
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7603855 0.703125
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8189852 0.6001157
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8660382 0.587963
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6699667 0.6290509
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7606479 0.5642361
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8307353 0.6018519
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.871536 0.4386574
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6699667 0.6290509
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7351861 0.6296296
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8136383 0.6203704
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8823414 0.5486111
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6699667 0.6290509
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7654962 0.6805556
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8312405 0.5943287
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8695219 0.568287
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6699667 0.6290509
## 2 2 25 0.7600706 0.6475694
## 3 3 25 0.7941007 0.5850694
## 4 5 25 0.8688920 0.4895833
## 5 1 20 0.6699667 0.6290509
## 6 2 20 0.7603855 0.7031250
## 7 3 20 0.8189852 0.6001157
## 8 5 20 0.8660382 0.5879630
## 9 1 15 0.6699667 0.6290509
## 10 2 15 0.7606479 0.5642361
## 11 3 15 0.8307353 0.6018519
## 12 5 15 0.8715360 0.4386574
## 13 1 10 0.6699667 0.6290509
## 14 2 10 0.7351861 0.6296296
## 15 3 10 0.8136383 0.6203704
## 16 5 10 0.8823414 0.5486111
## 17 1 5 0.6699667 0.6290509
## 18 2 5 0.7654962 0.6805556
## 19 3 5 0.8312405 0.5943287
## 20 5 5 0.8695219 0.5682870
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7603855 0.703125
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6853645 0.7251157
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7513843 0.6961806
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8081011 0.6493056
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.872461 0.6857639
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6853645 0.5914352
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7625374 0.6018519
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8170564 0.6493056
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8740356 0.6724537
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6853645 0.5914352
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7622815 0.671875
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8056146 0.6244213
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8784575 0.5266204
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6853645 0.5844907
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7503412 0.6782407
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.812851 0.6209491
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8660644 0.609375
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6853645 0.7251157
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7552288 0.615162
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8086981 0.6990741
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.849092 0.5792824
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6853645 0.7251157
## 2 2 25 0.7513843 0.6961806
## 3 3 25 0.8081011 0.6493056
## 4 5 25 0.8724610 0.6857639
## 5 1 20 0.6853645 0.5914352
## 6 2 20 0.7625374 0.6018519
## 7 3 20 0.8170564 0.6493056
## 8 5 20 0.8740356 0.6724537
## 9 1 15 0.6853645 0.5914352
## 10 2 15 0.7622815 0.6718750
## 11 3 15 0.8056146 0.6244213
## 12 5 15 0.8784575 0.5266204
## 13 1 10 0.6853645 0.5844907
## 14 2 10 0.7503412 0.6782407
## 15 3 10 0.8128510 0.6209491
## 16 5 10 0.8660644 0.6093750
## 17 1 5 0.6853645 0.7251157
## 18 2 5 0.7552288 0.6151620
## 19 3 5 0.8086981 0.6990741
## 20 5 5 0.8490920 0.5792824
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6853645 0.7251157
## 17 1 5 0.6853645 0.7251157
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7627736 0.5810185
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8130609 0.6076389
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8494791 0.6614583
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8902797 0.6354167
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7627736 0.5810185
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7978468 0.6412037
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8553837 0.5972222
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8915656 0.5486111
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7627736 0.5810185
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8136055 0.6030093
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8603501 0.6331019
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.901669 0.7025463
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7627736 0.5810185
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8172532 0.6215278
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8682425 0.5578704
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8887052 0.6168981
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7627736 0.5810185
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8117882 0.6221065
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8541765 0.6238426
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8919527 0.6099537
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7627736 0.5810185
## 2 2 25 0.8130609 0.6076389
## 3 3 25 0.8494791 0.6614583
## 4 5 25 0.8902797 0.6354167
## 5 1 20 0.7627736 0.5810185
## 6 2 20 0.7978468 0.6412037
## 7 3 20 0.8553837 0.5972222
## 8 5 20 0.8915656 0.5486111
## 9 1 15 0.7627736 0.5810185
## 10 2 15 0.8136055 0.6030093
## 11 3 15 0.8603501 0.6331019
## 12 5 15 0.9016690 0.7025463
## 13 1 10 0.7627736 0.5810185
## 14 2 10 0.8172532 0.6215278
## 15 3 10 0.8682425 0.5578704
## 16 5 10 0.8887052 0.6168981
## 17 1 5 0.7627736 0.5810185
## 18 2 5 0.8117882 0.6221065
## 19 3 5 0.8541765 0.6238426
## 20 5 5 0.8919527 0.6099537
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.901669 0.7025463
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.774504 0.6412037
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.825992 0.6359954
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8618459 0.6649306
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8951937 0.6747685
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7740579 0.6429398
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8320081 0.619213
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.863696 0.6568287
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8924316 0.6203704
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.774504 0.6412037
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8345799 0.6238426
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8702435 0.6736111
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8941505 0.7037037
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.774504 0.6412037
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.831293 0.6377315
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8639387 0.681713
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9034207 0.6527778
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.774504 0.6412037
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8228035 0.6388889
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8810948 0.6579861
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9088595 0.6851852
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7745040 0.6412037
## 2 2 25 0.8259920 0.6359954
## 3 3 25 0.8618459 0.6649306
## 4 5 25 0.8951937 0.6747685
## 5 1 20 0.7740579 0.6429398
## 6 2 20 0.8320081 0.6192130
## 7 3 20 0.8636960 0.6568287
## 8 5 20 0.8924316 0.6203704
## 9 1 15 0.7745040 0.6412037
## 10 2 15 0.8345799 0.6238426
## 11 3 15 0.8702435 0.6736111
## 12 5 15 0.8941505 0.7037037
## 13 1 10 0.7745040 0.6412037
## 14 2 10 0.8312930 0.6377315
## 15 3 10 0.8639387 0.6817130
## 16 5 10 0.9034207 0.6527778
## 17 1 5 0.7745040 0.6412037
## 18 2 5 0.8228035 0.6388889
## 19 3 5 0.8810948 0.6579861
## 20 5 5 0.9088595 0.6851852
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8941505 0.7037037
## id C NC pred obs
## 1 1 0.4634543 0.5365457 NC C
## 2 32 0.3354558 0.6645442 NC NC
## 3 40 0.6617289 0.3382711 C C
## 4 41 0.4384980 0.5615020 NC C
## 5 51 0.3868150 0.6131850 NC NC
## 6 103 0.5405117 0.4594883 C NC
## id C NC pred obs
## 1 1 0.4504463 0.5495537 NC C
## 2 32 0.3551662 0.6448338 NC NC
## 3 40 0.4934246 0.5065754 NC C
## 4 41 0.4504463 0.5495537 NC C
## 5 51 0.3799965 0.6200035 NC NC
## 6 103 0.3799965 0.6200035 NC NC
## id C NC pred obs
## 1 1 0.70192686 0.2980731 C C
## 2 32 0.18879532 0.8112047 NC NC
## 3 40 0.13067740 0.8693226 NC C
## 4 41 0.26092525 0.7390747 NC C
## 5 51 0.11600801 0.8839920 NC NC
## 6 103 0.05426563 0.9457344 NC NC
## id C NC pred obs
## 1 1 0.7271445 0.2728555 C C
## 2 32 0.3207696 0.6792304 NC NC
## 3 40 0.6598500 0.3401500 C C
## 4 41 0.2146170 0.7853830 NC C
## 5 51 0.4108134 0.5891866 NC NC
## 6 103 0.1036997 0.8963003 NC NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 24 controls (perf_imgT2$obs C) > 36 cases (perf_imgT2$obs NC).
## Area under the curve: 0.7031
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 24 controls (perf_allT2$obs C) > 36 cases (perf_allT2$obs NC).
## Area under the curve: 0.7251
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 24 controls (perf_imgT1$obs C) > 36 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7025
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 24 controls (perf_all$obs C) > 36 cases (perf_all$obs NC).
## Area under the curve: 0.7037
## Area under the curve: 0.7031
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.4999711 0.375 0.5833 0.7917 0.6944 0.8333 0.9444
## Area under the curve: 0.7251
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.4263524 0.5417 0.7083 0.875 0.5556 0.7222 0.8611
## 0.3460922 0.7500 0.8750 1.000 0.3889 0.5556 0.7222
## Area under the curve: 0.7025
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.2054541 0.625 0.7917 0.9177 0.4167 0.5833 0.75
## Area under the curve: 0.7037
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.5580426 0.375 0.5833 0.7917 0.75 0.8611 0.9722
## massB massM nonmassB nonmassM
## 212 149 132 63
## massB massM nonmassB nonmassM
## 30 17 10 14
## massB massM nonmassB nonmassM
## 212 149 132 63
## massB massM nonmassB nonmassM
## 30 17 10 14
## massB massM nonmassB nonmassM
## 212 149 132 63
## massB massM nonmassB nonmassM
## 30 17 10 14
## 0.09178744 0.05
## -0.1382979 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2RGH_var" "ave_T210" "T2texture_correlation_nondir" "T2skew_F_r_i"
## [5] "T2var_F_r_i" "ave_T211" "ave_T27" "ave_T212"
## [9] "ave_T214" "ave_T23" "T2texture_energy_nondir" "ave_T25"
## [13] "ave_T28" "ave_T20" "T2texture_diffvariance_nondir" "T2max_F_r_i"
## [17] "ave_T218" "T2kurt_F_r_i" "ave_T217" "ave_T29"
## [21] "T2RGH_mean" "ave_T26" "ave_T24" "T2texture_sumentropy_nondir"
## [25] "T2texture_variance_nondir" "T2texture_inversediffmoment_nondir" "ave_T215" "T2_lesionSI"
## [29] "ave_T219" "T2min_F_r_i" "ave_T22" "ave_T216"
## [33] "T2grad_margin_var" "T2texture_sumaverage_nondir" "ave_T213" "T2_lesionSIstd"
## 0.1004785 0.05
## -0.06382979 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_var" "T2grad_margin_var" "T2RGH_mean" "T2max_F_r_i"
## [5] "T2texture_inversediffmoment_nondir" "LMSIR" "T2wSI_predicted" "ave_T210"
## [9] "T2texture_sumvariance_nondir" "ave_T218" "ave_T20" "ave_T212"
## [13] "T2var_F_r_i" "T2texture_energy_nondir" "ave_T22" "ave_T25"
## [17] "T2texture_contrast_nondir" "ave_T23" "T2min_F_r_i" "ave_T219"
## [21] "ave_T215" "ave_T216" "T2_lesionSI" "T2texture_correlation_nondir"
## [25] "ave_T217" "ave_T21" "ave_T213" "T2texture_entropy_nondir"
## [29] "T2skew_F_r_i" "ave_T29" "LMSIR_predicted" "ave_T28"
## [33] "T2kurt_F_r_i" "find_t2_signal_int"
## 0.09937888 0.05
## -0.006896552 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "circularity" "alpha_inside" "texture_sumvariance_nondir_post3"
## [4] "washoutRate_inside" "texture_inversediffmoment_nondir_post4" "texture_diffvariance_nondir_post1"
## [7] "iMax_Variance_uptake" "texture_correlation_nondir_post2" "texture_sumaverage_nondir_post4"
## [10] "edge_sharp_std" "kurt_F_r_i" "V2"
## [13] "V6" "earlySE7" "Vr_increasingRate_inside"
## [16] "dce3SE17" "dce2SE0" "V0"
## [19] "lateSE9" "V19" "skew_F_r_i"
## [22] "V18" "earlySE4" "dce2SE7"
## [25] "lateSE16" "texture_sumaverage_nondir_post1" "var_F_r_i"
## [28] "lateSE1" "texture_inversediffmoment_nondir_post3" "dce3SE5"
## [31] "max_RGH_var_k" "dce2SE14" "Tpeak_countor"
## [34] "lateSE0" "V7" "A_inside"
## 0.05 0.05
## 0.05263158 0.05
## -0.0625 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "irregularity" "SER_countor" "texture_sumvariance_nondir_post2"
## [4] "texture_sumaverage_nondir_post1" "texture_inversediffmoment_nondir_post2" "iiMin_change_Variance_uptake"
## [7] "T2texture_correlation_nondir" "T2RGH_var" "lateSE8"
## [10] "Kpeak_inside" "texture_sumvariance_nondir_post4" "beta_inside"
## [13] "Vr_decreasingRate_inside" "V17" "A_countor"
## [16] "var_F_r_i" "UptakeRate_inside" "texture_energy_nondir_post1"
## [19] "max_RGH_var" "kurt_F_r_i" "dce2SE5"
## [22] "V6" "texture_diffentropy_nondir_post1" "ave_T216"
## [25] "dce3SE17" "texture_contrast_nondir_post2" "dce2SE3"
## [28] "dce3SE9" "ave_T212" "V12"
## [31] "peakCr_inside" "maxCr_countor" "ave_T28"
## [34] "Vr_increasingRate_countor" "lateSE1" "ave_T20"
## [37] "T2texture_variance_nondir" "T2skew_F_r_i" "dce3SE10"
## [40] "peakVr_countor" "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 23 23 0132 5154279 3 massB BENIGN BREAST TISSUE Hyperintense
## 24 24 0132 5154279 3 massB BENIGN BREAST TISSUE Hyperintense
## 54 54 0220 6715021 5 massB RadialScar Slightly hyperintense
## 55 55 0220 6715021 5 massB FIBROADENOMA Slightly hyperintense
## 57 57 0232 6671713 5 nonmassB FIBROCYSTIC None
## 58 58 0232 6671713 5 nonmassB FIBROCYSTIC None
## 66 66 0266 5254958 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 74 74 0325 4696948 4 massB FIBROCYSTIC Hyperintense
## 87 87 0442 4936886 4 massB BENIGN BREAST TISSUE Slightly hyperintense
## 89 89 0462 5466989 3 nonmassM InvasiveDuctal Hypointense or not seen
## 90 90 0462 5466989 4 massB FIBROADENOMA Hyperintense
## 102 102 0552 4663314 4 massB ADENOSIS Slightly hyperintense
## 112 112 0580 6855384 4 massB FIBROADENOMA None
## 123 123 0624 4894714 5 massB FIBROCYSTIC Hypointense or not seen
## 139 139 0683 5226149 5 massM InvasiveDuctal None
## 172 172 0726 5304228 5 massM InvasiveDuctal Slightly hyperintense
## 188 188 0743 4827839 4 massM InvasiveDuctal Hypointense or not seen
## 209 209 0781 4738440 5 nonmassM InvasiveDuctal None
## 235 235 0812 4700538 5 massM InvasiveDuctal Hypointense or not seen
## 242 242 0818 5021762 4 massB DUCT PAPILLOMA None
## 250 250 0831 4633368 6 nonmassM InsituDuctal Slightly hyperintense
## 282 282 0867 5372277 5 nonmassM InvasiveDuctal None
## 287 287 0873 4956191 4 massB FIBROCYSTIC Hypointense or not seen
## 288 288 0873 4956191 4 massB FIBROCYSTIC Slightly hyperintense
## 292 292 0877 4724338 4 nonmassB ATYPICAL LOBULAR HYPERPLASIA None
## 293 293 0880 4809515 4 massB Papillary(focalAtypia) Slightly hyperintense
## 294 294 0880 6778829 3 massM InsituDuctal None
## 295 295 0880 6778829 3 nonmassM InsituDuctal None
## 296 296 0880 6778829 3 nonmassM InsituDuctal None
## 297 297 0880 4809515 4 massB AtypicalPapilloma Slightly hyperintense
## 299 299 0884 6876318 6 massM InvasiveDuctal None
## 300 300 0884 6876318 6 nonmassM InsituDuctal None
## 322 322 0952 7105222 4 nonmassB FOCAL USUAL DUCTAL HYPERPLASIA Hypointense or not seen
## 323 323 0952 7105222 4 nonmassB FIBROADENOMA Hyperintense
## 327 327 0965 6676125 3 massB FIBROADENOMA Slightly hyperintense
## 359 359 1071 7382882 4 nonmassM InsituDuctal None
## 360 360 1072 7554174 6 massM InvasiveDuctal Slightly hyperintense
## 361 361 1072 7554174 4 massB SCLEROSING PAPILLARY LESION Hypointense or not seen
## 373 373 1095 4378323 3 massB FIBROADENOMA Hyperintense
## 374 374 1095 4378323 5 nonmassM InsituDuctal None
## 383 383 2028 6702914 6 nonmassB FIBROCYSTIC Hypointense or not seen
## 384 384 2028 6702914 6 massM InvasiveDuctal None
## 385 385 2029 6716423 6 massB ADENOSIS None
## 398 398 2055 7041426 6 nonmassM InvasiveDuctal None
## 411 411 3004 7691918 4 nonmassB FIBROCYSTIC None
## 412 412 3004 7691918 4 nonmassB FIBROCYSTIC None
## 435 435 3046 7682447 4 massB FIBROADENOMA Hypointense or not seen
## 436 436 3046 7289130 4 massB FIBROADENOMA Hyperintense
## 437 437 3046 7682447 4 massB FIBROADENOMA Hypointense or not seen
## 457 457 3075 7064471 6 massM InvasiveDuctal None
## 458 458 3075 7064471 6 nonmassM InsituDuctal None
## 474 474 3097 6909883 4 massB ATYPICAL DUCTAL HYPERPLASIA Hypointense or not seen
## 475 475 4002 6993690 5 massB BENIGN BREAST TISSUE Hypointense or not seen
## 487 487 4023 7037125 4 massM InvasiveDuctal None
## 488 488 4023 7037125 4 massB ADENOSIS, COLUMNAR CELL CHANGES Hypointense or not seen
## 489 489 4023 7152678 4 massB BENIGN INTRAMAMMARY LYMPH NODE Hypointense or not seen
## 490 490 4023 7037125 4 massM InvasiveDuctal None
## 506 506 6001 4574766 6 nonmassM InvasiveDuctal None
## 513 513 6014 5101372 6 massM InvasiveDuctal None
## 570 570 6052 5369136 6 nonmassM InvasiveDuctal None
## 571 571 6054 5425486 5 massM InsituDuctal None
## 572 572 6054 5425486 5 massM InsituDuctal None
## 573 573 6054 5425486 5 massM InsituDuctal None
## 574 574 6054 5425486 5 massM InsituDuctal None
## 575 575 6054 5425486 5 massM InsituDuctal None
## 592 592 6233 7047121 6 massB FIBROADENOMA Hyperintense
## 604 604 7066 6715383 4 massB FIBROADENOMA None
## 605 605 7066 7395276 4 nonmassB COLUMNAR CELL CHANGES None
## 615 615 7096 6869668 3 massB FIBROADENOMA None
## 616 616 7096 6869668 3 massB FIBROADENOMA Hypointense or not seen
## 624 624 7159 5435020 4 nonmassM InvasiveLobular None
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6763657 0.7608871
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7699786 0.658871
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.818643 0.6895161
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8461222 0.6153226
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6763657 0.7641129
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7532429 0.7193548
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8090925 0.6903226
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8751028 0.5512097
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6763657 0.7608871
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7547444 0.678629
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8092022 0.6451613
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8438666 0.6217742
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6739113 0.7596774
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7747642 0.6947581
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8062198 0.6758065
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8726347 0.6427419
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6763657 0.7608871
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7558071 0.6556452
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8144677 0.6379032
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8526081 0.6475806
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6763657 0.7608871
## 2 2 25 0.7699786 0.6588710
## 3 3 25 0.8186430 0.6895161
## 4 5 25 0.8461222 0.6153226
## 5 1 20 0.6763657 0.7641129
## 6 2 20 0.7532429 0.7193548
## 7 3 20 0.8090925 0.6903226
## 8 5 20 0.8751028 0.5512097
## 9 1 15 0.6763657 0.7608871
## 10 2 15 0.7547444 0.6786290
## 11 3 15 0.8092022 0.6451613
## 12 5 15 0.8438666 0.6217742
## 13 1 10 0.6739113 0.7596774
## 14 2 10 0.7747642 0.6947581
## 15 3 10 0.8062198 0.6758065
## 16 5 10 0.8726347 0.6427419
## 17 1 5 0.6763657 0.7608871
## 18 2 5 0.7558071 0.6556452
## 19 3 5 0.8144677 0.6379032
## 20 5 5 0.8526081 0.6475806
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6763657 0.7641129
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.679115 0.846371
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7473536 0.7842742
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8019348 0.5721774
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8833027 0.5758065
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.679115 0.846371
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7419578 0.7608871
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8088114 0.6625
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8880677 0.6580645
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.679115 0.846371
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7575623 0.8084677
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8045332 0.6399194
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8464787 0.6987903
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.679115 0.7875
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.760099 0.7471774
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8151533 0.7435484
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8818972 0.7177419
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.679115 0.846371
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7605446 0.7201613
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.804115 0.7334677
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8626591 0.733871
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6791150 0.8463710
## 2 2 25 0.7473536 0.7842742
## 3 3 25 0.8019348 0.5721774
## 4 5 25 0.8833027 0.5758065
## 5 1 20 0.6791150 0.8463710
## 6 2 20 0.7419578 0.7608871
## 7 3 20 0.8088114 0.6625000
## 8 5 20 0.8880677 0.6580645
## 9 1 15 0.6791150 0.8463710
## 10 2 15 0.7575623 0.8084677
## 11 3 15 0.8045332 0.6399194
## 12 5 15 0.8464787 0.6987903
## 13 1 10 0.6791150 0.7875000
## 14 2 10 0.7600990 0.7471774
## 15 3 10 0.8151533 0.7435484
## 16 5 10 0.8818972 0.7177419
## 17 1 5 0.6791150 0.8463710
## 18 2 5 0.7605446 0.7201613
## 19 3 5 0.8041150 0.7334677
## 20 5 5 0.8626591 0.7338710
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.679115 0.846371
## 5 1 20 0.679115 0.846371
## 9 1 15 0.679115 0.846371
## 17 1 5 0.679115 0.846371
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7490881 0.7217742
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8073854 0.7689516
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8673692 0.7185484
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.886717 0.7495968
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7490881 0.7217742
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.813549 0.703629
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8440242 0.7064516
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8907278 0.7314516
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7491841 0.7217742
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8174432 0.7512097
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.848227 0.7310484
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8962881 0.7508065
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7490881 0.7217742
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8215432 0.7447581
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8569068 0.7596774
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8757884 0.733871
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7490881 0.7217742
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8183619 0.7564516
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8487686 0.7233871
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8775025 0.7923387
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7490881 0.7217742
## 2 2 25 0.8073854 0.7689516
## 3 3 25 0.8673692 0.7185484
## 4 5 25 0.8867170 0.7495968
## 5 1 20 0.7490881 0.7217742
## 6 2 20 0.8135490 0.7036290
## 7 3 20 0.8440242 0.7064516
## 8 5 20 0.8907278 0.7314516
## 9 1 15 0.7491841 0.7217742
## 10 2 15 0.8174432 0.7512097
## 11 3 15 0.8482270 0.7310484
## 12 5 15 0.8962881 0.7508065
## 13 1 10 0.7490881 0.7217742
## 14 2 10 0.8215432 0.7447581
## 15 3 10 0.8569068 0.7596774
## 16 5 10 0.8757884 0.7338710
## 17 1 5 0.7490881 0.7217742
## 18 2 5 0.8183619 0.7564516
## 19 3 5 0.8487686 0.7233871
## 20 5 5 0.8775025 0.7923387
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8775025 0.7923387
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7984519 0.7483871
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8358655 0.7548387
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8766797 0.7403226
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9225058 0.7483871
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7984519 0.7483871
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8420703 0.7673387
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8811773 0.7342742
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.9132638 0.7274194
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7984519 0.7483871
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8335893 0.7524194
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8766866 0.7697581
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9255361 0.7532258
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7984519 0.7483871
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8402465 0.7625
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8751577 0.7633065
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9217036 0.741129
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7984519 0.7483871
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8395884 0.7677419
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8768649 0.7633065
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9204626 0.7612903
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7984519 0.7483871
## 2 2 25 0.8358655 0.7548387
## 3 3 25 0.8766797 0.7403226
## 4 5 25 0.9225058 0.7483871
## 5 1 20 0.7984519 0.7483871
## 6 2 20 0.8420703 0.7673387
## 7 3 20 0.8811773 0.7342742
## 8 5 20 0.9132638 0.7274194
## 9 1 15 0.7984519 0.7483871
## 10 2 15 0.8335893 0.7524194
## 11 3 15 0.8766866 0.7697581
## 12 5 15 0.9255361 0.7532258
## 13 1 10 0.7984519 0.7483871
## 14 2 10 0.8402465 0.7625000
## 15 3 10 0.8751577 0.7633065
## 16 5 10 0.9217036 0.7411290
## 17 1 5 0.7984519 0.7483871
## 18 2 5 0.8395884 0.7677419
## 19 3 5 0.8768649 0.7633065
## 20 5 5 0.9204626 0.7612903
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8766866 0.7697581
## id C NC pred obs
## 1 23 0.4332146 0.5667854 NC NC
## 2 24 0.4332146 0.5667854 NC NC
## 3 54 0.3290334 0.6709666 NC NC
## 4 55 0.2248541 0.7751459 NC NC
## 5 57 0.3290334 0.6709666 NC NC
## 6 58 0.5194341 0.4805659 C NC
## id C NC pred obs
## 1 23 0.3099970 0.6900030 NC NC
## 2 24 0.3099970 0.6900030 NC NC
## 3 54 0.2589154 0.7410846 NC NC
## 4 55 0.2024799 0.7975201 NC NC
## 5 57 0.4035094 0.5964906 NC NC
## 6 58 0.6133157 0.3866843 C NC
## id C NC pred obs
## 1 23 0.40890222 0.5910978 NC NC
## 2 24 0.45046918 0.5495308 NC NC
## 3 54 0.08715890 0.9128411 NC NC
## 4 55 0.09480616 0.9051938 NC NC
## 5 57 0.46095529 0.5390447 NC NC
## 6 58 0.06305759 0.9369424 NC NC
## id C NC pred obs
## 1 23 0.8112861 0.18871388 C NC
## 2 24 0.2191945 0.78080550 NC NC
## 3 54 0.8873925 0.11260753 C NC
## 4 55 0.2823164 0.71768360 NC NC
## 5 57 0.9055688 0.09443119 C NC
## 6 58 0.6242090 0.37579095 C NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 55 controls (perf_imgT2$obs C) > 76 cases (perf_imgT2$obs NC).
## Area under the curve: 0.7311
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 55 controls (perf_allT2$obs C) > 76 cases (perf_allT2$obs NC).
## Area under the curve: 0.7897
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 55 controls (perf_imgT1$obs C) > 76 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7437
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 55 controls (perf_all$obs C) > 76 cases (perf_all$obs NC).
## Area under the curve: 0.7417
## Area under the curve: 0.7311
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.4319897 0.6182 0.7455 0.8545 0.5526 0.6579 0.7632
## Area under the curve: 0.7897
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.342046 0.7636 0.8545 0.9455 0.5263 0.6316 0.7368
## Area under the curve: 0.7437
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.4131759 0.5273 0.6545 0.7818 0.6579 0.7632 0.8553
## Area under the curve: 0.7417
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.5426628 0.4727 0.6 0.7273 0.7632 0.8421 0.9211
## massB massM nonmassB nonmassM
## 219 153 129 71
## massB massM nonmassB nonmassM
## 23 13 13 6
## massB massM nonmassB nonmassM
## 219 153 129 71
## massB massM nonmassB nonmassM
## 23 13 13 6
## massB massM nonmassB nonmassM
## 219 153 129 71
## massB massM nonmassB nonmassM
## 23 13 13 6
## -0.02970297 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2RGH_var" "T2texture_entropy_nondir" "ave_T210" "T2texture_correlation_nondir"
## [5] "ave_T211" "T2_lesionSIstd" "T2skew_F_r_i" "T2grad_margin"
## [9] "ave_T215" "T2mean_F_r_i" "ave_T20" "ave_T25"
## [13] "T2texture_inversediffmoment_nondir" "ave_T27" "ave_T24" "ave_T28"
## [17] "T2texture_sumentropy_nondir" "ave_T214" "T2kurt_F_r_i" "ave_T217"
## [21] "T2texture_sumvariance_nondir" "T2texture_diffentropy_nondir" "ave_T29" "ave_T26"
## [25] "ave_T22" "T2RGH_mean" "T2_lesionSI"
## -0.02985075 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_var" "T2kurt_F_r_i" "T2RGH_mean" "T2grad_margin_var"
## [5] "T2_lesionSIstd" "ave_T28" "find_t2_signal_int" "T2texture_inversediffmoment_nondir"
## [9] "T2texture_energy_nondir" "ave_T213" "T2max_F_r_i" "ave_T218"
## [13] "ave_T217" "ave_T24" "T2mean_F_r_i" "ave_T214"
## [17] "T2texture_sumaverage_nondir" "ave_T25" "T2texture_sumvariance_nondir" "T2texture_diffvariance_nondir"
## [21] "ave_T29" "ave_T210" "T2texture_variance_nondir" "ave_T215"
## [25] "ave_T22" "ave_T219" "T2texture_correlation_nondir" "LMSIR"
## [29] "T2grad_margin" "T2skew_F_r_i" "ave_T216" "T2_lesionSI"
## 0.1165644 0.05
## -0.125 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "irregularity" "texture_sumvariance_nondir_post1" "iiMin_change_Variance_uptake"
## [4] "SER_countor" "alpha_inside" "texture_energy_nondir_post2"
## [7] "texture_contrast_nondir_post2" "texture_sumaverage_nondir_post3" "V4"
## [10] "Tpeak_countor" "lateSE0" "earlySE13"
## [13] "UptakeRate_inside" "max_RGH_var" "lateSE18"
## [16] "texture_correlation_nondir_post2" "earlySE19" "texture_inversediffmoment_nondir_post4"
## [19] "dce2SE12" "V2" "mean_F_r_i"
## [22] "dce2SE1" "dce3SE5" "lateSE5"
## [25] "min_F_r_i" "dce2SE18" "dce2SE7"
## [28] "texture_diffentropy_nondir_post4" "lateSE3" "earlySE11"
## [31] "Vr_decreasingRate_countor" "texture_sumentropy_nondir_post4" "dce3SE7"
## [34] "V19" "texture_correlation_nondir_post3" "A_inside"
## 0.03184713 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "texture_variance_nondir_post2" "SER_inside" "texture_inversediffmoment_nondir_post4"
## [4] "V12" "texture_sumvariance_nondir_post2" "texture_energy_nondir_post2"
## [7] "V10" "V13" "texture_diffvariance_nondir_post3"
## [10] "lateSE11" "lateSE9" "T2var_F_r_i"
## [13] "ave_T210" "T2kurt_F_r_i" "ave_T29"
## [16] "T2texture_entropy_nondir" "T2texture_energy_nondir" "dce3SE17"
## [19] "lateSE7" "ivVariance" "var_F_r_i"
## [22] "T2RGH_mean" "lateSE13" "dce2SE13"
## [25] "T2texture_contrast_nondir" "dce3SE7" "dce3SE16"
## [28] "skew_F_r_i" "mean_F_r_i" "earlySE9"
## [31] "T2min_F_r_i" "texture_correlation_nondir_post1" "k_Max_Margin_Grad"
## [34] "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 33 33 0177 6996979 3 massM InsituDuctal Slightly hyperintense
## 34 34 0177 6996979 3 nonmassM InsituDuctal None
## 52 52 0207 4982884 4 massB FIBROSIS None
## 83 83 0420 6738142 3 nonmassM InsituDuctal Slightly hyperintense
## 93 93 0473 7364625 4 massB FIBROCYSTIC None
## 96 96 0510 7662547 4 nonmassB COLUMNAR CELL CHANGES None
## 97 97 0510 7662547 4 nonmassB COLUMNAR CELL CHANGES None
## 99 99 0519 4937737 4 massB FLAT EPITHELIAL ATYPIA None
## 121 121 0619 7250777 5 massM InvasiveDuctal None
## 122 122 0619 7250777 5 nonmassM InvasiveDuctal Hyperintense
## 124 124 0635 7092156 4 massM InvasiveDuctal Hypointense or not seen
## 127 127 0663 4804825 4 massB FIBROADENOMA Hyperintense
## 133 133 0668 6989634 4 nonmassM InsituDuctal None
## 146 146 0690 5180451 3 nonmassB FIBROCYSTIC None
## 147 147 0690 5180451 3 massB USUAL DUCTAL HYPERPLASIA Slightly hyperintense
## 148 148 0690 6681276 4 nonmassB COLUMNAR CELL CHANGES Hypointense or not seen
## 171 171 0724 5141876 5 massM InvasiveDuctal Hyperintense
## 198 198 0760 4750742 5 nonmassM InsituDuctal None
## 212 212 0758 4796378 4 massB FIBROCYSTIC Hyperintense
## 213 213 0758 4796378 4 massB FIBROCYSTIC Hyperintense
## 219 219 0790 4708057 4 nonmassB DUCT PAPILLOMA None
## 230 230 0803 5058195 5 massM InvasiveDuctal None
## 233 233 0809 5016014 4 massB FIBROCYSTIC Hyperintense
## 303 303 0888 6744887 5 massM InvasiveDuctal None
## 304 304 0896 6895982 4 massB FIBROADENOMA Slightly hyperintense
## 305 305 0898 5224531 4 massB DUCTAL HYPERPLASIA WITHOUT ATYPIA None
## 311 311 0921 6997232 4 massB FIBROCYSTIC Hypointense or not seen
## 318 318 0944 7742881 4 massM InsituDuctal Hypointense or not seen
## 319 319 0944 7092128 4 nonmassB BENIGN BREAST TISSUE None
## 325 325 0956 5062341 4 massB FIBROADENOMA Slightly hyperintense
## 326 326 0962 4755483 4 massB FIBROADENOMA Hyperintense
## 333 333 0995 6816787 4 nonmassB LARGE DUCT PAPILLOMA Hyperintense
## 334 334 0995 6816787 3 massB DUCT PAPILLOMA Slightly hyperintense
## 339 339 1006 4443563 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 368 368 1087 5360576 4 massB GRANULOMATOUS LOBULAR MASTITIS None
## 369 369 1087 5360576 4 massB GRANULOMATOUS LOBULAR MASTITIS None
## 404 404 2072 7256932 4 massM InvasiveDuctal None
## 407 407 2075 6985605 4 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
## 408 408 2075 6985605 4 massB FIBROADENOMA Hypointense or not seen
## 419 419 3011 6898308 4 nonmassB FIBROCYSTIC None
## 461 461 3077 7042083 4 nonmassB FIBROCYSTIC None
## 462 462 3077 7042083 4 massB FIBROCYSTIC Slightly hyperintense
## 480 480 4012 7002008 4 massB FOCAL USUAL DUCTAL HYPERPLASIA Hypointense or not seen
## 498 498 4043 7041465 6 nonmassM InvasiveDuctal None
## 509 509 6005 ACC108250 5 massM InvasiveLobular None
## 510 510 6005 ACC108250 5 massM InvasiveLobular None
## 511 511 6005 ACC108250 5 massM InvasiveLobular None
## 552 552 6040 5075204 5 massM InvasiveDuctal None
## 578 578 6100 6722170 5 massM InvasiveDuctal Hypointense or not seen
## 586 586 6150 7128025 4 nonmassB COLUMNAR CELL CHANGES None
## 597 597 7024 6805356 4 massB FIBROADENOMA Hypointense or not seen
## 601 601 7043 7119983 4 massB FIBROADENOMA Hyperintense
## 623 623 7151 7557684 2 massB HYPERPLASIA None
## 625 625 7165 5021830 3 massB ADENOSIS None
## 635 635 7201 5041620 4 nonmassB FIBROADENOMA None
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6790204 0.5804094
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7604936 0.5307018
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8035329 0.6074561
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.857765 0.625731
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6790204 0.5804094
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7362159 0.5986842
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.7922439 0.6052632
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8477076 0.625731
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6793411 0.5804094
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7509365 0.6111111
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.7835591 0.5453216
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8435319 0.5453216
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6790204 0.5804094
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.739346 0.6103801
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.7863108 0.6944444
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8591056 0.6374269
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6772886 0.4290936
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7515073 0.6418129
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.7909547 0.630848
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8462387 0.6681287
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6790204 0.5804094
## 2 2 25 0.7604936 0.5307018
## 3 3 25 0.8035329 0.6074561
## 4 5 25 0.8577650 0.6257310
## 5 1 20 0.6790204 0.5804094
## 6 2 20 0.7362159 0.5986842
## 7 3 20 0.7922439 0.6052632
## 8 5 20 0.8477076 0.6257310
## 9 1 15 0.6793411 0.5804094
## 10 2 15 0.7509365 0.6111111
## 11 3 15 0.7835591 0.5453216
## 12 5 15 0.8435319 0.5453216
## 13 1 10 0.6790204 0.5804094
## 14 2 10 0.7393460 0.6103801
## 15 3 10 0.7863108 0.6944444
## 16 5 10 0.8591056 0.6374269
## 17 1 5 0.6772886 0.4290936
## 18 2 5 0.7515073 0.6418129
## 19 3 5 0.7909547 0.6308480
## 20 5 5 0.8462387 0.6681287
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.7863108 0.6944444
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6893473 0.3991228
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7434126 0.6023392
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8009095 0.6125731
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8350267 0.5497076
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6893473 0.3991228
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7542847 0.5928363
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.7962464 0.5248538
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8735376 0.6410819
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6893473 0.3991228
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7485504 0.622807
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.7942003 0.6644737
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8529351 0.6403509
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6893473 0.3991228
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7350998 0.4122807
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8014034 0.5709064
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8503951 0.5635965
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6893473 0.3991228
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.746671 0.5913743
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8074713 0.6001462
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8558472 0.4663743
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6893473 0.3991228
## 2 2 25 0.7434126 0.6023392
## 3 3 25 0.8009095 0.6125731
## 4 5 25 0.8350267 0.5497076
## 5 1 20 0.6893473 0.3991228
## 6 2 20 0.7542847 0.5928363
## 7 3 20 0.7962464 0.5248538
## 8 5 20 0.8735376 0.6410819
## 9 1 15 0.6893473 0.3991228
## 10 2 15 0.7485504 0.6228070
## 11 3 15 0.7942003 0.6644737
## 12 5 15 0.8529351 0.6403509
## 13 1 10 0.6893473 0.3991228
## 14 2 10 0.7350998 0.4122807
## 15 3 10 0.8014034 0.5709064
## 16 5 10 0.8503951 0.5635965
## 17 1 5 0.6893473 0.3991228
## 18 2 5 0.7466710 0.5913743
## 19 3 5 0.8074713 0.6001462
## 20 5 5 0.8558472 0.4663743
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.7942003 0.6644737
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7831037 0.6732456
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8502668 0.7353801
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8771488 0.7339181
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9092134 0.6856725
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7831037 0.6732456
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8398373 0.6703216
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8768537 0.7434211
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.9132607 0.7426901
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7831037 0.6732456
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8426468 0.746345
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8721585 0.754386
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9007338 0.7266082
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7811602 0.6783626
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8393114 0.7368421
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8743586 0.752924
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9132928 0.7997076
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7831037 0.6732456
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8412228 0.7404971
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8702342 0.7726608
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9004451 0.7368421
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7831037 0.6732456
## 2 2 25 0.8502668 0.7353801
## 3 3 25 0.8771488 0.7339181
## 4 5 25 0.9092134 0.6856725
## 5 1 20 0.7831037 0.6732456
## 6 2 20 0.8398373 0.6703216
## 7 3 20 0.8768537 0.7434211
## 8 5 20 0.9132607 0.7426901
## 9 1 15 0.7831037 0.6732456
## 10 2 15 0.8426468 0.7463450
## 11 3 15 0.8721585 0.7543860
## 12 5 15 0.9007338 0.7266082
## 13 1 10 0.7811602 0.6783626
## 14 2 10 0.8393114 0.7368421
## 15 3 10 0.8743586 0.7529240
## 16 5 10 0.9132928 0.7997076
## 17 1 5 0.7831037 0.6732456
## 18 2 5 0.8412228 0.7404971
## 19 3 5 0.8702342 0.7726608
## 20 5 5 0.9004451 0.7368421
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9132928 0.7997076
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7604423 0.7076023
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8240199 0.7039474
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8600934 0.627193
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8977512 0.6915205
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7604423 0.7076023
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8250013 0.6403509
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8563218 0.6747076
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8930111 0.7076023
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7610453 0.7061404
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8204023 0.7068713
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.858554 0.6725146
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9035945 0.6637427
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7604423 0.7076023
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8302481 0.6849415
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8515753 0.6951754
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.901651 0.6549708
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7603589 0.7076023
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8236607 0.748538
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8647822 0.6564327
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9011635 0.6929825
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7604423 0.7076023
## 2 2 25 0.8240199 0.7039474
## 3 3 25 0.8600934 0.6271930
## 4 5 25 0.8977512 0.6915205
## 5 1 20 0.7604423 0.7076023
## 6 2 20 0.8250013 0.6403509
## 7 3 20 0.8563218 0.6747076
## 8 5 20 0.8930111 0.7076023
## 9 1 15 0.7610453 0.7061404
## 10 2 15 0.8204023 0.7068713
## 11 3 15 0.8585540 0.6725146
## 12 5 15 0.9035945 0.6637427
## 13 1 10 0.7604423 0.7076023
## 14 2 10 0.8302481 0.6849415
## 15 3 10 0.8515753 0.6951754
## 16 5 10 0.9016510 0.6549708
## 17 1 5 0.7603589 0.7076023
## 18 2 5 0.8236607 0.7485380
## 19 3 5 0.8647822 0.6564327
## 20 5 5 0.9011635 0.6929825
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8236607 0.748538
## id C NC pred obs
## 1 33 0.4418755 0.5581245 NC C
## 2 34 0.6274420 0.3725580 C C
## 3 52 0.3578501 0.6421499 NC NC
## 4 83 0.4682128 0.5317872 NC C
## 5 93 0.2605829 0.7394171 NC NC
## 6 96 0.5010980 0.4989020 C NC
## id C NC pred obs
## 1 33 0.54864425 0.4513557 C C
## 2 34 0.62848981 0.3715102 C C
## 3 52 -0.04291709 1.0429171 NC NC
## 4 83 0.54864425 0.4513557 C C
## 5 93 0.21144414 0.7885559 NC NC
## 6 96 0.62134156 0.3786584 C NC
## id C NC pred obs
## 1 33 0.342423839 0.6575762 NC C
## 2 34 0.149383063 0.8506169 NC C
## 3 52 0.505883813 0.4941162 C NC
## 4 83 0.044883123 0.9551169 NC C
## 5 93 -0.017740981 1.0177410 NC NC
## 6 96 0.007402913 0.9925971 NC NC
## id C NC pred obs
## 1 33 0.1390917 0.8609083 NC C
## 2 34 0.1636962 0.8363038 NC C
## 3 52 0.5383023 0.4616977 C NC
## 4 83 0.3999752 0.6000248 NC C
## 5 93 0.3952478 0.6047522 NC NC
## 6 96 0.2110812 0.7889188 NC NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 74 controls (perf_imgT2$obs C) > 112 cases (perf_imgT2$obs NC).
## Area under the curve: 0.7196
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 74 controls (perf_allT2$obs C) > 112 cases (perf_allT2$obs NC).
## Area under the curve: 0.7346
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 74 controls (perf_imgT1$obs C) > 112 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7548
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 74 controls (perf_all$obs C) > 112 cases (perf_all$obs NC).
## Area under the curve: 0.7387
## Area under the curve: 0.7196
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3362545 0.7162 0.8108 0.8919 0.4643 0.5625 0.6518
## Area under the curve: 0.7346
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.302529 0.8378 0.9054 0.973 0.3839 0.4732 0.5627
## Area under the curve: 0.7548
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.5811 0.6892 0.7973 0.6786 0.7589 0.8304
## Area under the curve: 0.7387
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3591493 0.6216 0.7297 0.8243 0.6161 0.6964 0.7768
## massB massM nonmassB nonmassM
## 226 149 128 70
## massB massM nonmassB nonmassM
## 16 17 14 7
## massB massM nonmassB nonmassM
## 226 149 128 70
## massB massM nonmassB nonmassM
## 16 17 14 7
## massB massM nonmassB nonmassM
## 226 149 128 70
## massB massM nonmassB nonmassM
## 16 17 14 7
## -0.0430622 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2texture_entropy_nondir" "ave_T210" "T2RGH_var" "T2RGH_mean"
## [5] "ave_T27" "T2texture_inversediffmoment_nondir" "T2grad_margin" "T2kurt_F_r_i"
## [9] "T2texture_energy_nondir" "ave_T21" "T2skew_F_r_i" "T2texture_contrast_nondir"
## [13] "T2texture_sumaverage_nondir" "ave_T215" "ave_T25" "ave_T216"
## [17] "ave_T219" "ave_T29" "T2max_F_r_i" "ave_T28"
## [21] "ave_T214" "T2texture_diffvariance_nondir" "T2texture_correlation_nondir" "T2texture_sumvariance_nondir"
## [25] "ave_T22" "ave_T212" "ave_T23" "ave_T26"
## [29] "ave_T213" "T2var_F_r_i" "T2min_F_r_i" "ave_T20"
## [33] "ave_T24" "T2_lesionSI"
## 0.1148936 0.05
## -0.03365385 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_mean" "T2RGH_var" "T2texture_entropy_nondir" "find_t2_signal_int"
## [5] "ave_T210" "LMSIR" "T2texture_correlation_nondir" "ave_T27"
## [9] "T2grad_margin_var" "T2texture_inversediffmoment_nondir" "ave_T211" "ave_T21"
## [13] "ave_T219" "ave_T20" "T2_lesionSI" "T2kurt_F_r_i"
## [17] "ave_T28" "ave_T215" "ave_T24" "ave_T214"
## [21] "ave_T23" "ave_T216" "T2texture_contrast_nondir" "T2var_F_r_i"
## [25] "T2max_F_r_i" "T2texture_energy_nondir" "ave_T217" "T2texture_sumentropy_nondir"
## [29] "T2texture_sumvariance_nondir" "T2min_F_r_i" "T2texture_sumaverage_nondir" "T2skew_F_r_i"
## [33] "T2texture_diffentropy_nondir" "T2texture_diffvariance_nondir" "LMSIR_predicted" "ave_T218"
## [37] "ave_T25" "T2grad_margin" "ave_T29" "T2_lesionSIstd"
## 0.01923077 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "texture_sumvariance_nondir_post1" "circularity" "SER_inside"
## [4] "earlySE12" "max_RGH_mean" "iiMin_change_Variance_uptake"
## [7] "texture_inversediffmoment_nondir_post4" "texture_diffvariance_nondir_post3" "texture_energy_nondir_post4"
## [10] "maxVr_countor" "dce3SE8" "texture_variance_nondir_post3"
## [13] "V18" "edge_sharp_std" "V14"
## [16] "earlySE15" "V3" "A_countor"
## [19] "lateSE6" "dce2SE16" "texture_inversediffmoment_nondir_post2"
## [22] "Vr_increasingRate_countor" "var_F_r_i" "alpha_countor"
## [25] "lateSE14" "texture_correlation_nondir_post4" "lateSE4"
## [28] "V12" "texture_inversediffmoment_nondir_post3" "dce2SE8"
## [31] "V11" "V5" "peakCr_inside"
## [34] "dce2SE11" "maxCr_inside" "texture_entropy_nondir_post4"
## [37] "A_inside"
## -0.1088435 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "circularity" "earlySE5" "UptakeRate_inside" "Vr_increasingRate_countor"
## [5] "texture_sumaverage_nondir_post1" "texture_contrast_nondir_post1" "texture_correlation_nondir_post3" "earlySE19"
## [9] "texture_diffvariance_nondir_post3" "earlySE18" "ave_T218" "V4"
## [13] "T2texture_sumaverage_nondir" "lateSE17" "T2_lesionSIstd" "texture_diffentropy_nondir_post2"
## [17] "dce3SE0" "V17" "V5" "find_t2_signal_int"
## [21] "V3" "T2mean_F_r_i" "dce3SE7" "ave_T22"
## [25] "maxVr_countor" "dce3SE3" "SER_countor" "texture_energy_nondir_post1"
## [29] "Tpeak_countor" "V8" "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 11 11 0111 6907205 4 nonmassB DUCT PAPILLOMA Hypointense or not seen
## 12 12 0114 6896014 4 massM InvasiveDuctal None
## 82 82 0409 5161803 4 massB BENIGN BREAST TISSUE None
## 91 91 0463 7626269 4 massB FLORID HYPERPLASIA Hypointense or not seen
## 110 110 0576 6905042 4 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
## 115 115 0603 4593568 4 nonmassB FIBROSIS None
## 118 118 0613 4681594 4 nonmassM InsituDuctal None
## 119 119 0613 4681594 3 nonmassB BENIGN BREAST TISSUE None
## 135 135 0673 4585908 4 massB FIBROCYSTIC Hypointense or not seen
## 138 138 0682 5050826 6 nonmassM InsituDuctal None
## 145 145 0689 5205923 2 massB COLUMNAR CELL CHANGES Hyperintense
## 149 149 0691 5178056 5 massM InvasiveDuctal Hypointense or not seen
## 150 150 0691 5178056 5 massM InvasiveDuctal Hypointense or not seen
## 168 168 0721 4961869 6 massM InvasiveDuctal Hyperintense
## 178 178 0729 4805710 4 massB ATYPICAL LOBULAR HYPERPLASIA None
## 182 182 0735 5276000 5 massM InvasiveDuctal None
## 186 186 0742 5329785 4 massB DUCT PAPILLOMA None
## 187 187 0742 5329785 4 nonmassB DUCT PAPILLOMA None
## 189 189 0744 4848278 5 massM InvasiveDuctal None
## 191 191 0748 4940559 6 massM ATYPICAL DUCTAL HYPERPLASIA None
## 195 195 0755 5059877 4 nonmassM InsituDuctal None
## 196 196 0755 5059877 4 nonmassB BENIGN BREAST TISSUE None
## 252 252 0837 4559849 5 massM InvasiveDuctal None
## 276 276 0861 5053396 5 massM InvasiveDuctal Hypointense or not seen
## 283 283 0870 5141888 6 nonmassM InvasiveLobular None
## 302 302 0887 6794529 4 massB FIBROCYSTIC Hypointense or not seen
## 316 316 0943 5395204 4 nonmassM InsituDuctal None
## 317 317 0943 5395204 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 320 320 0950 6931716 5 massM InvasiveDuctal Hypointense or not seen
## 321 321 0950 6931716 5 nonmassM InvasiveDuctal None
## 338 338 1004 6801264 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 363 363 1078 7105247 4 nonmassB DENSE FIBROSIS None
## 364 364 1078 7105247 4 nonmassB DENSE FIBROSIS None
## 377 377 2007 7366811 4 nonmassB FIBROADENOMA Hypointense or not seen
## 395 395 2051 6712632 6 massM InsituDuctal None
## 396 396 2051 6712632 6 nonmassB FIBROCYSTIC None
## 397 397 2053 6776964 6 massM InvasiveDuctal None
## 423 423 3021 7019819 4 massB BENIGN BREAST TISSUE None
## 430 430 3033 5016967 5 massM InvasiveDuctal None
## 456 456 3073 7043941 6 nonmassM IN SITU PAPILLARY CARCINOMA None
## 499 499 4044 7066571 4 massB FIBROADENOMATOID Hyperintense
## 500 500 4044 7066571 4 massB FOCAL CELLULAR STROMA Hyperintense
## 501 501 4044 7066571 4 massB FIBROADENOMA Slightly hyperintense
## 502 502 4045 7092118 4 massB FIBROADENOMA None
## 516 516 6017 5086121 6 massM InvasiveLobular None
## 517 517 6017 5086121 2 massB FIBROADENOMA Hyperintense
## 558 558 6044 5078981 5 massB FIBROCYSTIC None
## 559 559 6044 5078981 5 massM InvasiveDuctal None
## 583 583 6117 5154282 3 massB FIBROADENOMA Hyperintense
## 584 584 6141 7044114 2 massB FIBROADENOMA Hyperintense
## 598 598 7029 7014263 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 612 612 7086 6938067 4 massM InsituDuctal None
## 613 613 7088 7066921 3 nonmassB FIBROCYSTIC None
## 621 621 7105 7837892 4 massM InvasiveDuctal Slightly hyperintense
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6682661 0.6791667
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7464979 0.6798611
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.7941916 0.6625
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8506179 0.6972222
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6682661 0.6791667
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7482844 0.6666667
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8094446 0.6493056
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8633426 0.6152778
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6682661 0.6791667
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7549338 0.6597222
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8037884 0.7256944
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8604404 0.6354167
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6682661 0.6791667
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7426347 0.6625
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.79414 0.6388889
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8502696 0.6819444
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6682661 0.6791667
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7470139 0.6618056
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.7844465 0.6270833
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8612917 0.6402778
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6682661 0.6791667
## 2 2 25 0.7464979 0.6798611
## 3 3 25 0.7941916 0.6625000
## 4 5 25 0.8506179 0.6972222
## 5 1 20 0.6682661 0.6791667
## 6 2 20 0.7482844 0.6666667
## 7 3 20 0.8094446 0.6493056
## 8 5 20 0.8633426 0.6152778
## 9 1 15 0.6682661 0.6791667
## 10 2 15 0.7549338 0.6597222
## 11 3 15 0.8037884 0.7256944
## 12 5 15 0.8604404 0.6354167
## 13 1 10 0.6682661 0.6791667
## 14 2 10 0.7426347 0.6625000
## 15 3 10 0.7941400 0.6388889
## 16 5 10 0.8502696 0.6819444
## 17 1 5 0.6682661 0.6791667
## 18 2 5 0.7470139 0.6618056
## 19 3 5 0.7844465 0.6270833
## 20 5 5 0.8612917 0.6402778
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8037884 0.7256944
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6750638 0.3881944
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7640147 0.6083333
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8049171 0.6722222
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.863491 0.5513889
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6750638 0.3881944
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7562947 0.69375
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8163197 0.65
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8689343 0.6895833
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6750638 0.3881944
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7616671 0.6152778
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.7950365 0.5881944
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8758868 0.6298611
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6750638 0.3881944
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7457305 0.625
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8208665 0.6395833
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8632201 0.5375
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6750638 0.3881944
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7531731 0.6166667
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8110247 0.6527778
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8671155 0.6694444
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6750638 0.3881944
## 2 2 25 0.7640147 0.6083333
## 3 3 25 0.8049171 0.6722222
## 4 5 25 0.8634910 0.5513889
## 5 1 20 0.6750638 0.3881944
## 6 2 20 0.7562947 0.6937500
## 7 3 20 0.8163197 0.6500000
## 8 5 20 0.8689343 0.6895833
## 9 1 15 0.6750638 0.3881944
## 10 2 15 0.7616671 0.6152778
## 11 3 15 0.7950365 0.5881944
## 12 5 15 0.8758868 0.6298611
## 13 1 10 0.6750638 0.3881944
## 14 2 10 0.7457305 0.6250000
## 15 3 10 0.8208665 0.6395833
## 16 5 10 0.8632201 0.5375000
## 17 1 5 0.6750638 0.3881944
## 18 2 5 0.7531731 0.6166667
## 19 3 5 0.8110247 0.6527778
## 20 5 5 0.8671155 0.6694444
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7562947 0.69375
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7755979 0.6826389
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8349715 0.6708333
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8659482 0.6506944
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8998594 0.6888889
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7749078 0.6666667
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8193187 0.6618056
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8594987 0.6833333
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.89123 0.6840278
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7744628 0.6736111
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8243686 0.6666667
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8540103 0.6819444
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8934873 0.6972222
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7763782 0.6819444
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8299925 0.6916667
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.867509 0.6861111
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8943645 0.7319444
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7755979 0.6826389
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8250587 0.6666667
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8601243 0.6840278
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8914364 0.6666667
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7755979 0.6826389
## 2 2 25 0.8349715 0.6708333
## 3 3 25 0.8659482 0.6506944
## 4 5 25 0.8998594 0.6888889
## 5 1 20 0.7749078 0.6666667
## 6 2 20 0.8193187 0.6618056
## 7 3 20 0.8594987 0.6833333
## 8 5 20 0.8912300 0.6840278
## 9 1 15 0.7744628 0.6736111
## 10 2 15 0.8243686 0.6666667
## 11 3 15 0.8540103 0.6819444
## 12 5 15 0.8934873 0.6972222
## 13 1 10 0.7763782 0.6819444
## 14 2 10 0.8299925 0.6916667
## 15 3 10 0.8675090 0.6861111
## 16 5 10 0.8943645 0.7319444
## 17 1 5 0.7755979 0.6826389
## 18 2 5 0.8250587 0.6666667
## 19 3 5 0.8601243 0.6840278
## 20 5 5 0.8914364 0.6666667
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8943645 0.7319444
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7468075 0.6215278
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8220532 0.6666667
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8476511 0.6736111
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8892501 0.6256944
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7468075 0.6215278
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8186995 0.6590278
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8435041 0.6638889
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8873088 0.6659722
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7468075 0.6215278
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8174677 0.6798611
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.84531 0.6611111
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8722622 0.66875
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7468075 0.6215278
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8188285 0.6645833
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8421562 0.5881944
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8875345 0.6263889
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7468075 0.6215278
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8179707 0.6763889
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.86144 0.6777778
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8807819 0.6625
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7468075 0.6215278
## 2 2 25 0.8220532 0.6666667
## 3 3 25 0.8476511 0.6736111
## 4 5 25 0.8892501 0.6256944
## 5 1 20 0.7468075 0.6215278
## 6 2 20 0.8186995 0.6590278
## 7 3 20 0.8435041 0.6638889
## 8 5 20 0.8873088 0.6659722
## 9 1 15 0.7468075 0.6215278
## 10 2 15 0.8174677 0.6798611
## 11 3 15 0.8453100 0.6611111
## 12 5 15 0.8722622 0.6687500
## 13 1 10 0.7468075 0.6215278
## 14 2 10 0.8188285 0.6645833
## 15 3 10 0.8421562 0.5881944
## 16 5 10 0.8875345 0.6263889
## 17 1 5 0.7468075 0.6215278
## 18 2 5 0.8179707 0.6763889
## 19 3 5 0.8614400 0.6777778
## 20 5 5 0.8807819 0.6625000
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8174677 0.6798611
## id C NC pred obs
## 1 11 0.2872801 0.7127199 NC NC
## 2 12 0.3787448 0.6212552 NC C
## 3 82 0.3311468 0.6688532 NC NC
## 4 91 0.3310456 0.6689544 NC NC
## 5 110 0.4606282 0.5393718 NC NC
## 6 115 0.5914819 0.4085181 C NC
## id C NC pred obs
## 1 11 -0.1132676 1.1132676 NC NC
## 2 12 0.4221221 0.5778779 NC C
## 3 82 0.3306742 0.6693258 NC NC
## 4 91 0.4114521 0.5885479 NC NC
## 5 110 0.8285758 0.1714242 C NC
## 6 115 0.4114521 0.5885479 NC NC
## id C NC pred obs
## 1 11 0.025857243 0.97414276 NC NC
## 2 12 0.983080910 0.01691909 C C
## 3 82 0.361941255 0.63805875 NC NC
## 4 91 0.209443690 0.79055631 NC NC
## 5 110 0.006977669 0.99302233 NC NC
## 6 115 0.516792013 0.48320799 C NC
## id C NC pred obs
## 1 11 0.07604433 0.9239557 NC NC
## 2 12 0.77460015 0.2253998 C C
## 3 82 0.60733120 0.3926688 C NC
## 4 91 0.17154165 0.8284583 NC NC
## 5 110 0.07604433 0.9239557 NC NC
## 6 115 0.19482341 0.8051766 NC NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 98 controls (perf_imgT2$obs C) > 142 cases (perf_imgT2$obs NC).
## Area under the curve: 0.7211
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 98 controls (perf_allT2$obs C) > 142 cases (perf_allT2$obs NC).
## Area under the curve: 0.7246
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 98 controls (perf_imgT1$obs C) > 142 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7436
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 98 controls (perf_all$obs C) > 142 cases (perf_all$obs NC).
## Area under the curve: 0.7242
## Area under the curve: 0.7211
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3362545 0.7347 0.8163 0.8878 0.4718 0.5563 0.6408
## Area under the curve: 0.7246
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.302529 0.8469 0.9082 0.9592 0.3873 0.4648 0.5423
## Area under the curve: 0.7436
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.5612 0.6531 0.7449 0.6831 0.7535 0.8239
## Area under the curve: 0.7242
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3988443 0.551 0.6531 0.7449 0.669 0.7394 0.8099
## massB massM nonmassB nonmassM
## 225 147 127 69
## massB massM nonmassB nonmassM
## 17 19 15 8
## massB massM nonmassB nonmassM
## 225 147 127 69
## massB massM nonmassB nonmassM
## 17 19 15 8
## massB massM nonmassB nonmassM
## 225 147 127 69
## massB massM nonmassB nonmassM
## 17 19 15 8
## -0.04368932 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2texture_energy_nondir" "ave_T211" "T2max_F_r_i" "ave_T210"
## [5] "T2texture_sumaverage_nondir" "ave_T216" "T2grad_margin" "ave_T25"
## [9] "ave_T20" "T2_lesionSIstd" "T2texture_correlation_nondir" "T2kurt_F_r_i"
## [13] "ave_T23" "ave_T219" "T2texture_diffvariance_nondir" "ave_T26"
## [17] "ave_T215" "T2texture_inversediffmoment_nondir" "ave_T21" "T2min_F_r_i"
## [21] "ave_T29" "T2grad_margin_var" "T2_lesionSI" "T2RGH_var"
## [25] "ave_T213" "T2texture_diffentropy_nondir" "ave_T217" "T2texture_sumvariance_nondir"
## [29] "ave_T24" "ave_T212" "T2mean_F_r_i"
## -0.02392344 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_mean" "T2texture_correlation_nondir" "T2skew_F_r_i" "ave_T213" "T2texture_sumaverage_nondir"
## [6] "T2texture_energy_nondir" "T2texture_diffentropy_nondir" "T2wSI_predicted" "ave_T25" "ave_T20"
## [11] "ave_T216" "ave_T218" "T2_lesionSIstd" "T2max_F_r_i" "T2grad_margin_var"
## [16] "ave_T21" "ave_T211" "LMSIR" "ave_T29" "ave_T28"
## [21] "ave_T27" "T2texture_entropy_nondir" "LMSIR_predicted" "ave_T210" "T2kurt_F_r_i"
## [26] "ave_T24" "T2texture_sumentropy_nondir" "ave_T26" "ave_T22" "ave_T219"
## [31] "ave_T214" "ave_T215" "T2grad_margin" "find_t2_signal_int"
## 0.01851852 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "irregularity" "texture_sumvariance_nondir_post1" "SER_inside" "iiMin_change_Variance_uptake"
## [5] "skew_F_r_i" "max_F_r_i" "earlySE12" "texture_sumaverage_nondir_post3"
## [9] "lateSE11" "alpha_countor" "V19" "kurt_F_r_i"
## [13] "beta_inside" "Vr_decreasingRate_inside" "dce3SE13" "texture_energy_nondir_post3"
## [17] "texture_contrast_nondir_post2" "texture_correlation_nondir_post4" "dce2SE7" "texture_diffentropy_nondir_post1"
## [21] "V0" "dce2SE16" "V2" "lateSE8"
## [25] "lateSE4" "dce3SE10" "V18" "texture_sumvariance_nondir_post4"
## [29] "dce3SE6" "lateSE19" "lateSE12" "Slope_ini_inside"
## [33] "dce3SE0" "lateSE9" "A_inside"
## 0.06711409 0.05
## -0.05035971 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "irregularity" "texture_variance_nondir_post1" "edge_sharp_std"
## [4] "Vr_post_1_countor" "var_F_r_i" "earlySE0"
## [7] "lateSE13" "V11" "V15"
## [10] "texture_inversediffmoment_nondir_post4" "dce2SE8" "dce3SE6"
## [13] "texture_diffvariance_nondir_post3" "T2texture_energy_nondir" "texture_correlation_nondir_post3"
## [16] "peakCr_inside" "T2grad_margin" "V12"
## [19] "dce3SE2" "T2texture_variance_nondir" "V14"
## [22] "V10" "min_F_r_i" "texture_diffentropy_nondir_post3"
## [25] "texture_sumvariance_nondir_post1" "Kpeak_countor" "lateSE8"
## [28] "earlySE3" "ivVariance" "ave_T213"
## [31] "edge_sharp_mean" "dce2SE13" "dce2SE18"
## [34] "lateSE19" "ave_T217" "T2skew_F_r_i"
## [37] "earlySE19" "T2var_F_r_i" "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 10 10 0102 4755778 4 massB FIBROCYSTIC Hyperintense
## 69 69 0277 5077098 5 nonmassM InsituDuctal Hypointense or not seen
## 72 72 0293 7491268 4 nonmassB BENIGN BREAST TISSUE None
## 81 81 0388 7395410 5 massM InvasiveDuctal None
## 92 92 0465 4885863 2 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 95 95 0503 6697826 3 massM InvasiveDuctal Hyperintense
## 101 101 0551 4804820 4 massB FIBROEPITHELIAL Slightly hyperintense
## 108 108 0572 4681582 4 nonmassM InvasiveDuctal None
## 109 109 0573 5142109 4 nonmassB COLUMNAR CELL CHANGES None
## 128 128 0664 7081071 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA Hypointense or not seen
## 155 155 0707 5184832 4 nonmassB COMPLEX PAPILLARY LESION Hypointense or not seen
## 156 156 0707 5184832 4 nonmassB COMPLEX PAPILLARY LESION Hypointense or not seen
## 184 184 0737 4559808 3 massM InsituDuctal Hyperintense
## 199 199 0764 5088503 5 massM InvasiveDuctal None
## 200 200 0764 5088503 5 massM InvasiveDuctal None
## 202 202 0767 5306672 4 massB ATYPICAL PAPILLARY LESION None
## 205 205 0775 5437780 3 massB BENIGN BREAST TISSUE Slightly hyperintense
## 206 206 0775 5437780 3 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
## 207 207 0775 5437780 3 nonmassB BENIGN BREAST TISSUE Slightly hyperintense
## 210 210 0782 4775699 5 massM InvasiveDuctal None
## 243 243 0827 4985128 4 massM INSITUPAPILLARYCARCINOMA None
## 244 244 0827 4985128 4 nonmassM INSITUPAPILLARYCARCINOMA None
## 245 245 0827 4985128 4 massB USUAL DUCTAL HYPERPLASIA None
## 247 247 0829 5264139 5 massM InvasiveDuctal Hypointense or not seen
## 255 255 0843 4798594 4 massB FIBROCYSTIC None
## 256 256 0843 6792402 4 massB FIBROCYSTIC None
## 274 274 0857 4870283 4 massB FIBROCYSTIC Hypointense or not seen
## 275 275 0857 5013393 2 massM InsituDuctal Hypointense or not seen
## 289 289 0875 7141879 4 massB DUCT PAPILLOMA None
## 290 290 0875 5396107 4 nonmassB PAPILLARY LESION None
## 345 345 1021 6760795 4 massB FIBROADENOMA Hypointense or not seen
## 352 352 1050 7296806 3 nonmassB DENSE FIBROSIS None
## 370 370 1090 4288694 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA Slightly hyperintense
## 371 371 1092 4951061 6 massB InsituLobular None
## 372 372 1092 4951061 4 nonmassB InsituLobular None
## 381 381 2024 5190122 6 nonmassM InsituDuctal Hypointense or not seen
## 382 382 2027 5465838 6 massM InsituDuctal Hyperintense
## 401 401 2068 7559583 5 massM InvasiveDuctal Hypointense or not seen
## 420 420 3017 7014437 4 nonmassB FOCAL HYPERPLASIA Slightly hyperintense
## 425 425 3025 7103914 4 massB FIBROADENOMA Hyperintense
## 428 428 3030 7642998 4 massB BENIGN BREAST TISSUE Slightly hyperintense
## 454 454 3072 7054863 6 nonmassM InsituDuctal None
## 473 473 3093 7438787 4 massB BENIGN BREAST TISSUE None
## 481 481 4017 6979356 4 massB USUAL DUCTAL HYPERPLASIA Hypointense or not seen
## 482 482 4017 6979356 4 massB USUAL DUCTAL HYPERPLASIA Hypointense or not seen
## 505 505 4055 7439091 4 massB PSEUDOANGIOMATOUS STROMAL HYPERPLASIA None
## 507 507 6004 ACC108249 6 massM InvasiveLobular Hypointense or not seen
## 508 508 6004 ACC108249 5 nonmassM InvasiveLobular None
## 544 544 6037 5043444 5 massM InvasiveDuctal None
## 545 545 6037 5043444 5 massM InvasiveDuctal None
## 549 549 6039 ACC109197 5 massM InsituDuctal Hyperintense
## 550 550 6039 ACC109197 5 nonmassM InsituDuctal None
## 551 551 6039 ACC109197 5 massM InsituDuctal Hyperintense
## 555 555 6042 4504274 3 massM InvasiveDuctal Hypointense or not seen
## 556 556 6042 4504274 3 massM InvasiveDuctal Hypointense or not seen
## 566 566 6047 5275305 6 nonmassM Adenocarcinoma None
## 582 582 6114 5148523 6 nonmassB BENIGN BREAST TISSUE None
## 620 620 7104 6941351 5 massM InvasiveDuctal None
## 636 636 7220 7288789 4 nonmassB FIBROCYSTIC Hypointense or not seen
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6739268 0.6197917
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7539457 0.5405093
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8161301 0.6550926
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8888757 0.5341435
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6734204 0.6244213
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7416811 0.556713
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8206873 0.6064815
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8528777 0.6296296
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6739268 0.6197917
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7576152 0.5439815
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.812717 0.5873843
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8598156 0.5949074
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6739268 0.6197917
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7636324 0.6168981
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.7973222 0.5711806
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8780579 0.5972222
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6739268 0.6197917
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7580492 0.6064815
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8132957 0.6157407
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8719881 0.5972222
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6739268 0.6197917
## 2 2 25 0.7539457 0.5405093
## 3 3 25 0.8161301 0.6550926
## 4 5 25 0.8888757 0.5341435
## 5 1 20 0.6734204 0.6244213
## 6 2 20 0.7416811 0.5567130
## 7 3 20 0.8206873 0.6064815
## 8 5 20 0.8528777 0.6296296
## 9 1 15 0.6739268 0.6197917
## 10 2 15 0.7576152 0.5439815
## 11 3 15 0.8127170 0.5873843
## 12 5 15 0.8598156 0.5949074
## 13 1 10 0.6739268 0.6197917
## 14 2 10 0.7636324 0.6168981
## 15 3 10 0.7973222 0.5711806
## 16 5 10 0.8780579 0.5972222
## 17 1 5 0.6739268 0.6197917
## 18 2 5 0.7580492 0.6064815
## 19 3 5 0.8132957 0.6157407
## 20 5 5 0.8719881 0.5972222
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8161301 0.6550926
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.675196 0.4751157
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7522227 0.5179398
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8036156 0.490162
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8684764 0.5850694
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.675196 0.4751157
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7567406 0.521412
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8043258 0.5549769
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8548572 0.6261574
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.675196 0.5700231
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7580558 0.5497685
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8039773 0.4739583
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8623014 0.5063657
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.675196 0.4751157
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7568918 0.4762731
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8024253 0.5509259
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8596709 0.5324074
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.675196 0.5179398
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7470604 0.515625
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8053977 0.5659722
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8617753 0.5104167
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6751960 0.4751157
## 2 2 25 0.7522227 0.5179398
## 3 3 25 0.8036156 0.4901620
## 4 5 25 0.8684764 0.5850694
## 5 1 20 0.6751960 0.4751157
## 6 2 20 0.7567406 0.5214120
## 7 3 20 0.8043258 0.5549769
## 8 5 20 0.8548572 0.6261574
## 9 1 15 0.6751960 0.5700231
## 10 2 15 0.7580558 0.5497685
## 11 3 15 0.8039773 0.4739583
## 12 5 15 0.8623014 0.5063657
## 13 1 10 0.6751960 0.4751157
## 14 2 10 0.7568918 0.4762731
## 15 3 10 0.8024253 0.5509259
## 16 5 10 0.8596709 0.5324074
## 17 1 5 0.6751960 0.5179398
## 18 2 5 0.7470604 0.5156250
## 19 3 5 0.8053977 0.5659722
## 20 5 5 0.8617753 0.5104167
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8548572 0.6261574
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.8120791 0.6631944
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8530684 0.7077546
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8782486 0.7199074
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9188302 0.7164352
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.8120462 0.662037
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8447299 0.7118056
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8741517 0.7349537
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.9015152 0.7175926
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.8121975 0.6770833
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8494318 0.7112269
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8781171 0.7233796
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9145754 0.6643519
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.8116188 0.6799769
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8410932 0.7146991
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8760588 0.7210648
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9126552 0.6909722
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.8120791 0.6631944
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8465778 0.7164352
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8779659 0.7384259
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9163379 0.7789352
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.8120791 0.6631944
## 2 2 25 0.8530684 0.7077546
## 3 3 25 0.8782486 0.7199074
## 4 5 25 0.9188302 0.7164352
## 5 1 20 0.8120462 0.6620370
## 6 2 20 0.8447299 0.7118056
## 7 3 20 0.8741517 0.7349537
## 8 5 20 0.9015152 0.7175926
## 9 1 15 0.8121975 0.6770833
## 10 2 15 0.8494318 0.7112269
## 11 3 15 0.8781171 0.7233796
## 12 5 15 0.9145754 0.6643519
## 13 1 10 0.8116188 0.6799769
## 14 2 10 0.8410932 0.7146991
## 15 3 10 0.8760588 0.7210648
## 16 5 10 0.9126552 0.6909722
## 17 1 5 0.8120791 0.6631944
## 18 2 5 0.8465778 0.7164352
## 19 3 5 0.8779659 0.7384259
## 20 5 5 0.9163379 0.7789352
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9163379 0.7789352
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.805332 0.3310185
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8424742 0.6701389
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8693182 0.6695602
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9108204 0.6215278
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.805332 0.3310185
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8492871 0.6521991
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8730403 0.6666667
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.9172519 0.6643519
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.805332 0.3310185
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8500566 0.6869213
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8813592 0.7216435
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.909834 0.6672454
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.805332 0.3310185
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8480048 0.6944444
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8748224 0.671875
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9010088 0.6863426
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.8047533 0.3321759
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8512731 0.6591435
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8746186 0.7048611
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9221512 0.6782407
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.8053320 0.3310185
## 2 2 25 0.8424742 0.6701389
## 3 3 25 0.8693182 0.6695602
## 4 5 25 0.9108204 0.6215278
## 5 1 20 0.8053320 0.3310185
## 6 2 20 0.8492871 0.6521991
## 7 3 20 0.8730403 0.6666667
## 8 5 20 0.9172519 0.6643519
## 9 1 15 0.8053320 0.3310185
## 10 2 15 0.8500566 0.6869213
## 11 3 15 0.8813592 0.7216435
## 12 5 15 0.9098340 0.6672454
## 13 1 10 0.8053320 0.3310185
## 14 2 10 0.8480048 0.6944444
## 15 3 10 0.8748224 0.6718750
## 16 5 10 0.9010088 0.6863426
## 17 1 5 0.8047533 0.3321759
## 18 2 5 0.8512731 0.6591435
## 19 3 5 0.8746186 0.7048611
## 20 5 5 0.9221512 0.6782407
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8813592 0.7216435
## id C NC pred obs
## 1 10 0.173683825 0.8263162 NC NC
## 2 69 0.153238211 0.8467618 NC C
## 3 72 0.532763569 0.4672364 C NC
## 4 81 0.634166055 0.3658339 C C
## 5 92 0.006389876 0.9936101 NC NC
## 6 95 0.463105244 0.5368948 NC C
## id C NC pred obs
## 1 10 0.27935526 0.7206447 NC NC
## 2 69 0.52149257 0.4785074 C C
## 3 72 0.54686662 0.4531334 C NC
## 4 81 0.88186991 0.1181301 C C
## 5 92 0.41356202 0.5864380 NC NC
## 6 95 0.08475441 0.9152456 NC C
## id C NC pred obs
## 1 10 0.4963563 0.5036437 NC NC
## 2 69 0.2297114 0.7702886 NC C
## 3 72 0.3318701 0.6681299 NC NC
## 4 81 0.7369471 0.2630529 C C
## 5 92 0.1694308 0.8305692 NC NC
## 6 95 0.5068589 0.4931411 C C
## id C NC pred obs
## 1 10 0.3470170 0.6529830 NC NC
## 2 69 0.1827666 0.8172334 NC C
## 3 72 0.1727402 0.8272598 NC NC
## 4 81 0.5800385 0.4199615 C C
## 5 92 0.3803388 0.6196612 NC NC
## 6 95 0.2147703 0.7852297 NC C
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 125 controls (perf_imgT2$obs C) > 174 cases (perf_imgT2$obs NC).
## Area under the curve: 0.6968
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 125 controls (perf_allT2$obs C) > 174 cases (perf_allT2$obs NC).
## Area under the curve: 0.6997
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 125 controls (perf_imgT1$obs C) > 174 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7497
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 125 controls (perf_all$obs C) > 174 cases (perf_all$obs NC).
## Area under the curve: 0.7188
## Area under the curve: 0.6968
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.4328689 0.568 0.648 0.736 0.6092 0.6782 0.7471
## Area under the curve: 0.6997
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3022951 0.8 0.864 0.92 0.3908 0.4655 0.5402
## Area under the curve: 0.7497
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.584 0.672 0.752 0.6782 0.7414 0.8046
## Area under the curve: 0.7188
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3988443 0.544 0.624 0.704 0.6954 0.7586 0.8161
## massB massM nonmassB nonmassM
## 211 152 126 71
## massB massM nonmassB nonmassM
## 31 14 16 6
## massB massM nonmassB nonmassM
## 211 152 126 71
## massB massM nonmassB nonmassM
## 31 14 16 6
## massB massM nonmassB nonmassM
## 211 152 126 71
## massB massM nonmassB nonmassM
## 31 14 16 6
## 0.0462963 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2RGH_var" "T2texture_correlation_nondir" "ave_T210" "T2texture_energy_nondir"
## [5] "T2kurt_F_r_i" "T2grad_margin_var" "T2max_F_r_i" "T2texture_inversediffmoment_nondir"
## [9] "ave_T21" "T2skew_F_r_i" "ave_T25" "T2_lesionSIstd"
## [13] "ave_T215" "ave_T22" "ave_T20" "T2mean_F_r_i"
## [17] "T2grad_margin" "T2texture_sumentropy_nondir" "ave_T29" "ave_T24"
## [21] "ave_T213" "ave_T214" "T2RGH_mean" "ave_T217"
## [25] "T2min_F_r_i" "ave_T212" "T2texture_variance_nondir" "ave_T219"
## [29] "ave_T216" "ave_T27" "ave_T211" "ave_T28"
## [33] "T2texture_diffvariance_nondir" "T2texture_sumvariance_nondir" "T2_lesionSI"
## 0.04716981 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "ave_T210" "T2RGH_mean" "find_t2_signal_int" "T2RGH_var"
## [5] "T2texture_energy_nondir" "T2grad_margin_var" "T2max_F_r_i" "T2texture_inversediffmoment_nondir"
## [9] "T2texture_correlation_nondir" "LMSIR" "T2skew_F_r_i" "ave_T211"
## [13] "T2_lesionSI" "ave_T22" "T2texture_contrast_nondir" "ave_T218"
## [17] "ave_T212" "ave_T20" "ave_T29" "T2texture_sumaverage_nondir"
## [21] "ave_T24" "ave_T21" "ave_T26" "ave_T25"
## [25] "T2kurt_F_r_i" "T2_lesionSIstd" "ave_T214" "ave_T215"
## [29] "LMSIR_predicted" "T2texture_sumvariance_nondir" "ave_T28" "ave_T217"
## [33] "ave_T216" "T2texture_diffentropy_nondir" "T2min_F_r_i"
## 0.0875 0.05
## -0.006849315 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "var_F_r_i" "earlySE7" "Tpeak_countor" "min_F_r_i"
## [5] "V8" "V19" "texture_correlation_nondir_post2" "texture_sumaverage_nondir_post2"
## [9] "iMax_Variance_uptake" "texture_sumvariance_nondir_post4" "beta_inside" "V15"
## [13] "earlySE2" "texture_diffentropy_nondir_post1" "Vr_post_1_inside" "lateSE12"
## [17] "iiiMax_Margin_Gradient" "dce2SE13" "dce3SE16" "skew_F_r_i"
## [21] "earlySE1" "earlySE19" "lateSE7" "maxCr_inside"
## [25] "texture_energy_nondir_post3" "V2" "V10" "earlySE10"
## [29] "peakVr_inside" "Slope_ini_countor" "A_inside"
## -0.09433962 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "texture_sumvariance_nondir_post1" "max_RGH_mean" "V0"
## [4] "texture_energy_nondir_post3" "V18" "lateSE11"
## [7] "ave_T20" "texture_contrast_nondir_post2" "maxVr_inside"
## [10] "lateSE12" "texture_sumentropy_nondir_post4" "dce2SE19"
## [13] "washoutRate_inside" "V17" "edge_sharp_std"
## [16] "dce3SE0" "ave_T214" "skew_F_r_i"
## [19] "earlySE2" "T2grad_margin_var" "texture_sumaverage_nondir_post2"
## [22] "ave_T21" "Vr_decreasingRate_countor" "lateSE16"
## [25] "dce3SE1" "texture_inversediffmoment_nondir_post2" "earlySE18"
## [28] "Vr_decreasingRate_inside" "UptakeRate_countor" "ave_T26"
## [31] "ave_T210" "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 3 3 0025 7002835 4 nonmassB DENSE FIBROSIS None
## 35 35 0180 4632561 4 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
## 36 36 0180 5254957 4 nonmassB FIBROADENOMA Hypointense or not seen
## 45 45 0197 6667696 4 nonmassB LobularHyperplasia Hypointense or not seen
## 46 46 0197 6667696 4 nonmassB LobularHyperplasia Hypointense or not seen
## 47 47 0197 6667696 4 massB LobularHyperplasia Slightly hyperintense
## 70 70 0280 5091695 4 massB BENIGN BREAST TISSUE None
## 73 73 0311 6677243 4 massB FIBROADENOMA None
## 75 75 0331 4722659 2 massB FIBROCYSTIC None
## 76 76 0331 7347095 4 massB FIBROCYSTIC Hyperintense
## 77 77 0331 7347095 4 massB capillary hemangioma None
## 100 100 0536 7786869 4 massB FIBROADENOMA Hypointense or not seen
## 114 114 0595 7441706 4 massB BENIGN BREAST TISSUE Hypointense or not seen
## 125 125 0651 4695822 4 massB FIBROADENOMA Hyperintense
## 130 130 0667 4864590 3 massB FIBROADENOMA Hypointense or not seen
## 131 131 0667 4864590 4 massM InsituDuctal Hyperintense
## 132 132 0667 6993980 4 nonmassM InsituDuctal Hyperintense
## 142 142 0687 1201 5 massM InvasiveDuctal Slightly hyperintense
## 143 143 0687 1201 5 nonmassM InvasiveDuctal Slightly hyperintense
## 144 144 0687 1201 5 massM InvasiveDuctal Slightly hyperintense
## 173 173 0727 4803733 4 massM InsituDuctal Slightly hyperintense
## 174 174 0728 5304244 6 massB FIBROADENOMA Slightly hyperintense
## 175 175 0728 5304244 4 massB DUCT PAPILLOMA WITH ATYPIA Hyperintense
## 176 176 0728 5304244 4 massB FIBROADENOMA None
## 177 177 0728 5304244 6 nonmassM InvasiveDuctal None
## 180 180 0731 5265417 4 massB DYSTROPHICCALCIFICATION Slightly hyperintense
## 190 190 0745 4881779 4 massM InvasiveDuctal None
## 214 214 0776 5352670 5 massB AtypicalCells Hypointense or not seen
## 215 215 0776 5352670 5 massM InvasiveDuctal None
## 226 226 0795 5188009 6 nonmassB ATYPICAL DUCTAL HYPERPLASIA Hypointense or not seen
## 236 236 0813 5378164 5 nonmassB FIBROCYSTIC None
## 237 237 0813 5378164 5 massM InvasiveLobular None
## 246 246 0828 4787730 6 massM InsituDuctal None
## 253 253 0839 4739257 4 massB BENIGN BREAST TISSUE None
## 254 254 0839 4739257 4 massB BENIGN BREAST TISSUE None
## 257 257 0844 4795902 4 nonmassM InvasiveDuctal None
## 258 258 0845 5433683 5 massM InvasiveLobular None
## 324 324 0954 7962026 4 massB ATYPICAL LOBULAR HYPERPLASIA None
## 340 340 1008 6745959 5 massM InsituDuctal None
## 341 341 1012 7629993 6 massM InvasiveDuctal None
## 342 342 1012 6940724 4 massB FIBROADENOMA Hypointense or not seen
## 343 343 1012 6940724 4 nonmassB FIBROADENOMA Hyperintense
## 365 365 1079 7417880 4 massM InsituDuctal None
## 366 366 1081 7078151 4 massB FIBROADENOMA Hyperintense
## 389 389 2042 4964619 6 massB LobularHyperplasia Hyperintense
## 390 390 2042 5186978 4 massB ATYPICAL DUCTAL HYPERPLASIA Hypointense or not seen
## 391 391 2042 7050570 4 massB ATYPICAL DUCTAL HYPERPLASIA None
## 403 403 2071 7594721 4 massM InvasiveDuctal Slightly hyperintense
## 417 417 3010 6828446 6 massM InvasiveDuctal None
## 463 463 3078 4836946 5 nonmassB InsituLobular None
## 470 470 3083 5345062 4 nonmassB BENIGN BREAST TISSUE None
## 471 471 3086 7715466 4 nonmassB BENIGN BREAST TISSUE None
## 472 472 3092 4462310 3 massB BENIGN BREAST TISSUE Hypointense or not seen
## 478 478 4008 7014565 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 479 479 4008 7014565 6 massB HYPERPLASIA None
## 491 491 4026 6998219 4 massB ATYPICAL DUCTAL HYPERPLASIA Hypointense or not seen
## 494 494 4039 7041331 6 nonmassM InvasiveDuctal None
## 524 524 6023 4697014 3 massB FIBROCYSTIC None
## 525 525 6023 4697014 3 massB SCLEROSING ADENOSIS None
## 531 531 6026 4888386 4 nonmassM InsituDuctal None
## 557 557 6043 5249778 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 576 576 6069 7581124 4 massB BENIGN BREAST TISSUE Hyperintense
## 577 577 6069 7581124 4 massB BENIGN BREAST TISSUE Hypointense or not seen
## 587 587 6164 6971531 4 massB BENIGN BREAST TISSUE Hypointense or not seen
## 588 588 6174 7009629 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 633 633 7193 7347138 4 nonmassB BENIGN BREAST TISSUE None
## 634 634 7193 7347138 4 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6774893 0.437234
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7518995 0.5558511
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.818206 0.6606383
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.850807 0.587234
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6774893 0.4409574
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7463108 0.5526596
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.7957246 0.5968085
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8514641 0.5521277
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6774893 0.4335106
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7394845 0.575
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8013267 0.5675532
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.857294 0.462234
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6774893 0.4409574
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7376815 0.5691489
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8057644 0.6106383
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8551649 0.6265957
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6774893 0.4335106
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7454458 0.5803191
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.7948597 0.5638298
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8578329 0.6446809
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6774893 0.4372340
## 2 2 25 0.7518995 0.5558511
## 3 3 25 0.8182060 0.6606383
## 4 5 25 0.8508070 0.5872340
## 5 1 20 0.6774893 0.4409574
## 6 2 20 0.7463108 0.5526596
## 7 3 20 0.7957246 0.5968085
## 8 5 20 0.8514641 0.5521277
## 9 1 15 0.6774893 0.4335106
## 10 2 15 0.7394845 0.5750000
## 11 3 15 0.8013267 0.5675532
## 12 5 15 0.8572940 0.4622340
## 13 1 10 0.6774893 0.4409574
## 14 2 10 0.7376815 0.5691489
## 15 3 10 0.8057644 0.6106383
## 16 5 10 0.8551649 0.6265957
## 17 1 5 0.6774893 0.4335106
## 18 2 5 0.7454458 0.5803191
## 19 3 5 0.7948597 0.5638298
## 20 5 5 0.8578329 0.6446809
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.818206 0.6606383
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.692406 0.4664894
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7531503 0.5398936
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.7951524 0.5835106
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8714721 0.5842391
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.692406 0.4739362
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7517398 0.5569149
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8036886 0.5978723
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8751381 0.5856383
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.692406 0.4739362
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7478077 0.5851064
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8041743 0.5824468
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8774867 0.6957447
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.692406 0.4664894
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7529374 0.5734043
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.7975809 0.6608696
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8634017 0.5340426
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.692406 0.4664894
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7508683 0.4829787
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.7998629 0.3820652
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8852976 0.5164894
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6924060 0.4664894
## 2 2 25 0.7531503 0.5398936
## 3 3 25 0.7951524 0.5835106
## 4 5 25 0.8714721 0.5842391
## 5 1 20 0.6924060 0.4739362
## 6 2 20 0.7517398 0.5569149
## 7 3 20 0.8036886 0.5978723
## 8 5 20 0.8751381 0.5856383
## 9 1 15 0.6924060 0.4739362
## 10 2 15 0.7478077 0.5851064
## 11 3 15 0.8041743 0.5824468
## 12 5 15 0.8774867 0.6957447
## 13 1 10 0.6924060 0.4664894
## 14 2 10 0.7529374 0.5734043
## 15 3 10 0.7975809 0.6608696
## 16 5 10 0.8634017 0.5340426
## 17 1 5 0.6924060 0.4664894
## 18 2 5 0.7508683 0.4829787
## 19 3 5 0.7998629 0.3820652
## 20 5 5 0.8852976 0.5164894
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8774867 0.6957447
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7435031 0.7111702
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8134888 0.6968085
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8430493 0.7382979
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8988104 0.7680851
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7432369 0.712234
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8127969 0.7276596
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8433088 0.7680851
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8954039 0.7106383
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7435031 0.7111702
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8184322 0.7361702
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8667217 0.7521277
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9106066 0.6696809
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7435031 0.7111702
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8160437 0.762234
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8593432 0.6755319
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9009328 0.6989362
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7432369 0.712234
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8157909 0.7297872
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8543133 0.7042553
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8895757 0.737234
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7435031 0.7111702
## 2 2 25 0.8134888 0.6968085
## 3 3 25 0.8430493 0.7382979
## 4 5 25 0.8988104 0.7680851
## 5 1 20 0.7432369 0.7122340
## 6 2 20 0.8127969 0.7276596
## 7 3 20 0.8433088 0.7680851
## 8 5 20 0.8954039 0.7106383
## 9 1 15 0.7435031 0.7111702
## 10 2 15 0.8184322 0.7361702
## 11 3 15 0.8667217 0.7521277
## 12 5 15 0.9106066 0.6696809
## 13 1 10 0.7435031 0.7111702
## 14 2 10 0.8160437 0.7622340
## 15 3 10 0.8593432 0.6755319
## 16 5 10 0.9009328 0.6989362
## 17 1 5 0.7432369 0.7122340
## 18 2 5 0.8157909 0.7297872
## 19 3 5 0.8543133 0.7042553
## 20 5 5 0.8895757 0.7372340
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8988104 0.7680851
## 7 3 20 0.8433088 0.7680851
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.721381 0.7111702
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7989781 0.7180851
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8539208 0.8042553
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8978656 0.7542553
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.721381 0.7111702
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8055914 0.7234043
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8475802 0.7888298
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8941731 0.6946809
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7356056 0.7276596
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8075674 0.7308511
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8421911 0.7255319
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.891392 0.6840426
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7356056 0.7276596
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8113398 0.7973404
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8384719 0.806383
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8804141 0.8132979
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.721381 0.7111702
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8112866 0.7398936
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8372477 0.7553191
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8940999 0.7287234
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7213810 0.7111702
## 2 2 25 0.7989781 0.7180851
## 3 3 25 0.8539208 0.8042553
## 4 5 25 0.8978656 0.7542553
## 5 1 20 0.7213810 0.7111702
## 6 2 20 0.8055914 0.7234043
## 7 3 20 0.8475802 0.7888298
## 8 5 20 0.8941731 0.6946809
## 9 1 15 0.7356056 0.7276596
## 10 2 15 0.8075674 0.7308511
## 11 3 15 0.8421911 0.7255319
## 12 5 15 0.8913920 0.6840426
## 13 1 10 0.7356056 0.7276596
## 14 2 10 0.8113398 0.7973404
## 15 3 10 0.8384719 0.8063830
## 16 5 10 0.8804141 0.8132979
## 17 1 5 0.7213810 0.7111702
## 18 2 5 0.8112866 0.7398936
## 19 3 5 0.8372477 0.7553191
## 20 5 5 0.8940999 0.7287234
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8804141 0.8132979
## id C NC pred obs
## 1 3 0.88942258 0.1105774 C NC
## 2 35 0.38672633 0.6132737 NC NC
## 3 36 0.41367518 0.5863248 NC NC
## 4 45 0.10158314 0.8984169 NC NC
## 5 46 -0.07545195 1.0754519 NC NC
## 6 47 0.19992723 0.8000728 NC NC
## id C NC pred obs
## 1 3 0.06911886 0.9308811 NC NC
## 2 35 0.26427587 0.7357241 NC NC
## 3 36 0.31186047 0.6881395 NC NC
## 4 45 0.08271013 0.9172899 NC NC
## 5 46 0.06982144 0.9301786 NC NC
## 6 47 0.69159676 0.3084032 C NC
## id C NC pred obs
## 1 3 0.02230927 0.9776907 NC NC
## 2 35 0.05785518 0.9421448 NC NC
## 3 36 0.26923832 0.7307617 NC NC
## 4 45 0.15071420 0.8492858 NC NC
## 5 46 0.05006409 0.9499359 NC NC
## 6 47 0.05971202 0.9402880 NC NC
## id C NC pred obs
## 1 3 0.1260982 0.8739018 NC NC
## 2 35 0.1298090 0.8701910 NC NC
## 3 36 0.1903567 0.8096433 NC NC
## 4 45 0.1050739 0.8949261 NC NC
## 5 46 0.1822576 0.8177424 NC NC
## 6 47 0.1295480 0.8704520 NC NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 145 controls (perf_imgT2$obs C) > 221 cases (perf_imgT2$obs NC).
## Area under the curve: 0.6905
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 145 controls (perf_allT2$obs C) > 221 cases (perf_allT2$obs NC).
## Area under the curve: 0.7024
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 145 controls (perf_imgT1$obs C) > 221 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7512
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 145 controls (perf_all$obs C) > 221 cases (perf_all$obs NC).
## Area under the curve: 0.7366
## Area under the curve: 0.6905
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.4328689 0.5793 0.6552 0.731 0.6199 0.6787 0.7421
## Area under the curve: 0.7024
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3022951 0.7862 0.8483 0.9034 0.4344 0.5023 0.5656
## Area under the curve: 0.7512
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.6 0.6759 0.7448 0.6697 0.7285 0.7873
## Area under the curve: 0.7366
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3988443 0.5448 0.6276 0.7034 0.7104 0.7692 0.8235
## massB massM nonmassB nonmassM
## 223 148 121 72
## massB massM nonmassB nonmassM
## 19 18 21 5
## massB massM nonmassB nonmassM
## 223 148 121 72
## massB massM nonmassB nonmassM
## 19 18 21 5
## massB massM nonmassB nonmassM
## 223 148 121 72
## massB massM nonmassB nonmassM
## 19 18 21 5
## 0.04807692 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2texture_correlation_nondir" "T2kurt_F_r_i" "T2grad_margin_var" "T2texture_entropy_nondir"
## [5] "T2RGH_var" "T2RGH_mean" "ave_T210" "T2var_F_r_i"
## [9] "ave_T27" "T2texture_sumaverage_nondir" "ave_T213" "ave_T211"
## [13] "ave_T28" "ave_T216" "T2texture_diffentropy_nondir" "T2texture_variance_nondir"
## [17] "ave_T219" "ave_T215" "ave_T24" "ave_T29"
## [21] "ave_T218" "ave_T217" "ave_T22" "T2min_F_r_i"
## [25] "T2max_F_r_i" "T2texture_energy_nondir" "ave_T212" "ave_T20"
## [29] "T2texture_sumentropy_nondir" "ave_T21" "T2texture_inversediffmoment_nondir" "T2_lesionSI"
## [33] "ave_T25" "ave_T26" "T2_lesionSIstd"
## -0.07329843 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_var" "T2kurt_F_r_i" "find_t2_signal_int" "T2grad_margin" "T2texture_diffvariance_nondir"
## [6] "ave_T27" "T2_lesionSIstd" "ave_T211" "T2texture_correlation_nondir" "ave_T214"
## [11] "T2mean_F_r_i" "LMSIR_predicted" "LMSIR" "ave_T24" "ave_T215"
## [16] "ave_T22" "ave_T217" "ave_T25" "T2texture_energy_nondir" "ave_T20"
## [21] "ave_T218" "ave_T213" "ave_T23" "ave_T210" "ave_T219"
## [26] "ave_T29" "T2max_F_r_i" "T2texture_sumaverage_nondir" "T2skew_F_r_i" "T2_lesionSI"
## -0.0952381 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "texture_sumvariance_nondir_post1" "circularity" "V13"
## [4] "texture_inversediffmoment_nondir_post3" "Kpeak_inside" "Vr_post_1_countor"
## [7] "kurt_F_r_i" "texture_contrast_nondir_post3" "earlySE8"
## [10] "Slope_ini_countor" "Vr_decreasingRate_inside" "texture_sumaverage_nondir_post2"
## [13] "lateSE2" "lateSE1" "V2"
## [16] "dce2SE7" "edge_sharp_std" "Vr_increasingRate_inside"
## [19] "texture_energy_nondir_post4" "earlySE16" "dce2SE11"
## [22] "lateSE13" "dce2SE4" "V8"
## [25] "dce3SE10" "alpha_inside" "dce2SE16"
## [28] "max_RGH_mean_k" "peakCr_countor" "ivVariance"
## [31] "max_RGH_var_k" "texture_sumvariance_nondir_post2" "A_inside"
## -0.1780822 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "SER_inside" "texture_variance_nondir_post3" "V16" "texture_correlation_nondir_post2"
## [5] "texture_energy_nondir_post4" "V11" "V10" "iMax_Variance_uptake"
## [9] "edge_sharp_std" "earlySE10" "earlySE19" "T2texture_inversediffmoment_nondir"
## [13] "texture_diffvariance_nondir_post3" "ave_T26" "dce2SE7" "earlySE11"
## [17] "ave_T212" "LMSIR_predicted" "Vr_decreasingRate_inside" "texture_sumentropy_nondir_post2"
## [21] "dce3SE0" "texture_entropy_nondir_post4" "earlySE17" "dce3SE6"
## [25] "earlySE14" "ave_T218" "V9" "dce2SE6"
## [29] "texture_correlation_nondir_post1" "min_F_r_i" "max_RGH_var_k" "dce3SE16"
## [33] "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 15 15 0122 5108281 3 massB Cyst None
## 16 16 0123 6909758 4 nonmassB COLUMNAR CELL CHANGES None
## 17 17 0123 6909758 4 nonmassB BENIGN BREAST TISSUE None
## 39 39 0103 6836585 5 massB PHYLLODES TUMOR None
## 42 42 0196 5289117 4 nonmassB SCLEROSING ADENOSIS Hypointense or not seen
## 43 43 0196 5289117 4 nonmassB ColumnarAlterationwoAtypia None
## 44 44 0196 5289117 4 nonmassB ColumnarAlterationwoAtypia Hypointense or not seen
## 50 50 0199 4362726 4 massB ATYPICAL LOBULAR HYPERPLASIA Hyperintense
## 78 78 0352 4785776 4 massB FIBROADENOMA Slightly hyperintense
## 79 79 0357 5137030 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 80 80 0376 4609403 4 massB BENIGN HAMARTOMA Slightly hyperintense
## 88 88 0456 6689214 4 massM InvasiveDuctal None
## 113 113 0586 5332925 4 nonmassM InsituDuctal Hypointense or not seen
## 137 137 0681 4999374 3 massB FIBROCYSTIC Slightly hyperintense
## 154 154 0705 4648471 5 massM InvasiveDuctal Slightly hyperintense
## 162 162 0714 5324209 5 massM InvasiveDuctal None
## 163 163 0714 5324209 5 massM InvasiveDuctal None
## 164 164 0714 5324209 5 nonmassM InsituDuctal None
## 166 166 0720 4965525 4 massB FIBROCYSTIC Slightly hyperintense
## 167 167 0720 4965525 4 nonmassB FIBROADENOMA Hypointense or not seen
## 169 169 0722 5366177 5 massM InvasiveDuctal Hyperintense
## 183 183 0736 4963473 4 massB BENIGN BREAST TISSUE Slightly hyperintense
## 192 192 0752 4940477 4 nonmassB BENIGN BREAST TISSUE None
## 193 193 0752 4940477 4 nonmassB FIBROCYSTIC None
## 194 194 0752 4940477 4 nonmassB BENIGN BREAST TISSUE None
## 203 203 0771 4680997 4 massB DUCT PAPILLOMA None
## 204 204 0771 4680997 4 massB DUCT PAPILLOMA None
## 208 208 0778 4794199 5 massB FIBROADENOMA Hypointense or not seen
## 251 251 0834 4614262 5 massM InvasiveDuctal None
## 260 260 0847 5064132 4 massM InvasiveDuctal Hyperintense
## 291 291 0876 4719378 4 massB BENIGN BREAST TISSUE None
## 328 328 0967 6938015 4 nonmassB BENIGN BREAST TISSUE None
## 329 329 0967 6938015 4 nonmassM InvasiveDuctal None
## 346 346 1024 6980462 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 347 347 1024 6980462 4 nonmassB DUCT PAPILLOMA WITH ATYPIA None
## 348 348 1025 6703528 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 350 350 1044 7366817 5 massM InvasiveDuctal None
## 355 355 1062 7408296 4 massB ATYPICAL LOBULAR HYPERPLASIA Hypointense or not seen
## 356 356 1062 7408296 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 362 362 1077 6890028 4 massB BENIGN BREAST TISSUE Slightly hyperintense
## 379 379 2017 7397047 6 massB RADIAL SCLEROSING LESION None
## 386 386 2033 6849696 6 massM InvasiveLobular None
## 387 387 2033 6849696 4 nonmassB ATYPICAL LOBULAR HYPERPLASIA None
## 394 394 2050 6689745 6 massM InvasiveDuctal None
## 429 429 3031 7106716 3 massB COLUMNAR CELL CHANGES Hypointense or not seen
## 433 433 3039 6894870 4 massB HYPERPLASIA None
## 483 483 4018 6983262 6 nonmassM InsituDuctal None
## 484 484 4019 7151338 4 massB BENIGN BREAST TISSUE Hyperintense
## 486 486 4021 6992707 4 nonmassB ADENOSIS Hypointense or not seen
## 532 532 6027 4770166 4 massB BENIGN BREAST TISSUE None
## 533 533 6027 4770166 4 nonmassB BENIGN BREAST TISSUE None
## 541 541 6035 5062962 5 massM InvasiveDuctal None
## 542 542 6035 5062962 5 massM InvasiveDuctal None
## 543 543 6035 5062962 5 massM InvasiveDuctal None
## 560 560 6045 5208117 6 massM InvasiveDuctal Hypointense or not seen
## 561 561 6045 5208117 6 massM InvasiveDuctal Hypointense or not seen
## 567 567 6048 5284266 6 massM InvasiveDuctal None
## 579 579 6101 5087078 4 nonmassB FIBROCYSTIC None
## 580 580 6101 7709238 6 massM InvasiveDuctal Hypointense or not seen
## 606 606 7076 7267446 3 nonmassM InsituDuctal None
## 607 607 7076 7267446 3 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 628 628 7186 5263507 6 massM InvasiveDuctal None
## 632 632 7192 7974056 4 nonmassB BENIGN BREAST TISSUE None
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.665037 0.7065217
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7605444 0.6516304
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.7962341 0.7146739
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8675211 0.7173913
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.665037 0.7065217
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7504889 0.7179348
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.7992799 0.6418478
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8484871 0.7467391
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.665037 0.7065217
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7625925 0.7396739
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.7876387 0.6326087
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8580669 0.6597826
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.665037 0.7065217
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7635174 0.7521739
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8051533 0.6554348
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8612051 0.7603261
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.665037 0.7065217
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7588597 0.738587
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8206726 0.6576087
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8924022 0.7434783
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6650370 0.7065217
## 2 2 25 0.7605444 0.6516304
## 3 3 25 0.7962341 0.7146739
## 4 5 25 0.8675211 0.7173913
## 5 1 20 0.6650370 0.7065217
## 6 2 20 0.7504889 0.7179348
## 7 3 20 0.7992799 0.6418478
## 8 5 20 0.8484871 0.7467391
## 9 1 15 0.6650370 0.7065217
## 10 2 15 0.7625925 0.7396739
## 11 3 15 0.7876387 0.6326087
## 12 5 15 0.8580669 0.6597826
## 13 1 10 0.6650370 0.7065217
## 14 2 10 0.7635174 0.7521739
## 15 3 10 0.8051533 0.6554348
## 16 5 10 0.8612051 0.7603261
## 17 1 5 0.6650370 0.7065217
## 18 2 5 0.7588597 0.7385870
## 19 3 5 0.8206726 0.6576087
## 20 5 5 0.8924022 0.7434783
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8612051 0.7603261
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6834567 0.6576087
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7487183 0.6434783
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8024313 0.401087
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8731567 0.5380435
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6834567 0.6576087
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7434263 0.7336957
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.7945098 0.6376812
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8711945 0.5831522
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6834567 0.6576087
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7390658 0.6554348
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.7982426 0.6972826
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8515394 0.6320652
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6834567 0.6576087
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.743968 0.6332952
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.7958311 0.7602975
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8595996 0.7079153
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6834567 0.6576087
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7362976 0.6704805
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.795732 0.6353261
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8592627 0.6157609
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6834567 0.6576087
## 2 2 25 0.7487183 0.6434783
## 3 3 25 0.8024313 0.4010870
## 4 5 25 0.8731567 0.5380435
## 5 1 20 0.6834567 0.6576087
## 6 2 20 0.7434263 0.7336957
## 7 3 20 0.7945098 0.6376812
## 8 5 20 0.8711945 0.5831522
## 9 1 15 0.6834567 0.6576087
## 10 2 15 0.7390658 0.6554348
## 11 3 15 0.7982426 0.6972826
## 12 5 15 0.8515394 0.6320652
## 13 1 10 0.6834567 0.6576087
## 14 2 10 0.7439680 0.6332952
## 15 3 10 0.7958311 0.7602975
## 16 5 10 0.8595996 0.7079153
## 17 1 5 0.6834567 0.6576087
## 18 2 5 0.7362976 0.6704805
## 19 3 5 0.7957320 0.6353261
## 20 5 5 0.8592627 0.6157609
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.7958311 0.7602975
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7741477 0.6668478
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.809778 0.6967391
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8490156 0.6782609
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8862381 0.6657609
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7749736 0.6717391
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8221855 0.6880435
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8539905 0.648913
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8903938 0.6119565
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7741477 0.6668478
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8235597 0.6679348
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8519952 0.6701087
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8989561 0.6815217
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7747027 0.6728261
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8268895 0.6722826
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8486258 0.648913
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8813161 0.6429348
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.775185 0.6717391
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8317653 0.6913043
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8480576 0.688587
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8764337 0.648913
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7741477 0.6668478
## 2 2 25 0.8097780 0.6967391
## 3 3 25 0.8490156 0.6782609
## 4 5 25 0.8862381 0.6657609
## 5 1 20 0.7749736 0.6717391
## 6 2 20 0.8221855 0.6880435
## 7 3 20 0.8539905 0.6489130
## 8 5 20 0.8903938 0.6119565
## 9 1 15 0.7741477 0.6668478
## 10 2 15 0.8235597 0.6679348
## 11 3 15 0.8519952 0.6701087
## 12 5 15 0.8989561 0.6815217
## 13 1 10 0.7747027 0.6728261
## 14 2 10 0.8268895 0.6722826
## 15 3 10 0.8486258 0.6489130
## 16 5 10 0.8813161 0.6429348
## 17 1 5 0.7751850 0.6717391
## 18 2 5 0.8317653 0.6913043
## 19 3 5 0.8480576 0.6885870
## 20 5 5 0.8764337 0.6489130
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.809778 0.6967391
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7747489 0.6744565
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8302854 0.6918478
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8503502 0.6793478
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9010703 0.6809783
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7747489 0.6744565
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8272793 0.6934783
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8616874 0.6967391
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.9051136 0.6706522
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7747489 0.6744565
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8183272 0.6820652
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8525304 0.6913043
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9006144 0.6728261
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7747489 0.6744565
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8211416 0.6684783
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8578885 0.6923913
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9029334 0.7043478
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7747489 0.6744565
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8239429 0.6744565
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8597384 0.7027174
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9078951 0.6826087
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7747489 0.6744565
## 2 2 25 0.8302854 0.6918478
## 3 3 25 0.8503502 0.6793478
## 4 5 25 0.9010703 0.6809783
## 5 1 20 0.7747489 0.6744565
## 6 2 20 0.8272793 0.6934783
## 7 3 20 0.8616874 0.6967391
## 8 5 20 0.9051136 0.6706522
## 9 1 15 0.7747489 0.6744565
## 10 2 15 0.8183272 0.6820652
## 11 3 15 0.8525304 0.6913043
## 12 5 15 0.9006144 0.6728261
## 13 1 10 0.7747489 0.6744565
## 14 2 10 0.8211416 0.6684783
## 15 3 10 0.8578885 0.6923913
## 16 5 10 0.9029334 0.7043478
## 17 1 5 0.7747489 0.6744565
## 18 2 5 0.8239429 0.6744565
## 19 3 5 0.8597384 0.7027174
## 20 5 5 0.9078951 0.6826087
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9029334 0.7043478
## id C NC pred obs
## 1 15 0.196432828 0.8035672 NC NC
## 2 16 0.278047423 0.7219526 NC NC
## 3 17 0.470620837 0.5293792 NC NC
## 4 39 0.797028216 0.2029718 C NC
## 5 42 0.188378981 0.8116210 NC NC
## 6 43 0.008427335 0.9915727 NC NC
## id C NC pred obs
## 1 15 0.2117757 0.7882243 NC NC
## 2 16 0.3048998 0.6951002 NC NC
## 3 17 NaN NaN <NA> NC
## 4 39 0.6531322 0.3468678 C NC
## 5 42 -0.1855096 1.1855096 NC NC
## 6 43 0.1856887 0.8143113 NC NC
## id C NC pred obs
## 1 15 0.4225243 0.57747574 NC NC
## 2 16 0.1485160 0.85148396 NC NC
## 3 17 0.3011237 0.69887633 NC NC
## 4 39 1.0251584 -0.02515839 C NC
## 5 42 0.8569211 0.14307888 C NC
## 6 43 0.1494937 0.85050629 NC NC
## id C NC pred obs
## 1 15 0.11112533 0.88887467 NC NC
## 2 16 0.09053201 0.90946799 NC NC
## 3 17 0.38879992 0.61120008 NC NC
## 4 39 0.98824827 0.01175173 C NC
## 5 42 0.30053442 0.69946558 NC NC
## 6 43 0.06491870 0.93508130 NC NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 168 controls (perf_imgT2$obs C) > 261 cases (perf_imgT2$obs NC).
## Area under the curve: 0.7005
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 168 controls (perf_allT2$obs C) > 259 cases (perf_allT2$obs NC).
## Area under the curve: 0.7088
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 168 controls (perf_imgT1$obs C) > 261 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7403
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 168 controls (perf_all$obs C) > 261 cases (perf_all$obs NC).
## Area under the curve: 0.7327
## Area under the curve: 0.7005
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3361978 0.7321 0.7917 0.8454 0.4828 0.5441 0.6015
## Area under the curve: 0.7088
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3002026 0.7975 0.8512 0.8988 0.4556 0.5174 0.5792
## Area under the curve: 0.7403
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.5833 0.6548 0.7262 0.6667 0.7241 0.7778
## Area under the curve: 0.7327
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3988443 0.5536 0.631 0.7024 0.7088 0.7625 0.8161
## massB massM nonmassB nonmassM
## 214 142 128 76
## massB massM nonmassB nonmassM
## 28 24 14 1
## massB massM nonmassB nonmassM
## 214 142 128 76
## massB massM nonmassB nonmassM
## 28 24 14 1
## massB massM nonmassB nonmassM
## 214 142 128 76
## massB massM nonmassB nonmassM
## 28 24 14 1
## 0.04455446 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2RGH_var" "T2texture_entropy_nondir" "ave_T211" "T2texture_correlation_nondir"
## [5] "ave_T210" "T2grad_margin_var" "T2texture_inversediffmoment_nondir" "ave_T27"
## [9] "T2skew_F_r_i" "T2texture_energy_nondir" "ave_T218" "T2kurt_F_r_i"
## [13] "ave_T21" "T2texture_diffentropy_nondir" "ave_T26" "ave_T22"
## [17] "ave_T216" "T2var_F_r_i" "ave_T23" "T2texture_sumentropy_nondir"
## [21] "ave_T24" "ave_T28" "ave_T213" "T2min_F_r_i"
## [25] "ave_T219" "ave_T212" "ave_T20" "ave_T214"
## [29] "T2RGH_mean" "T2texture_sumaverage_nondir" "ave_T215" "ave_T217"
## [33] "T2texture_contrast_nondir" "T2texture_sumvariance_nondir" "T2_lesionSI"
## 0.05825243 0.05
## -0.03092784 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_var" "T2texture_correlation_nondir" "ave_T211" "T2texture_energy_nondir"
## [5] "T2RGH_mean" "ave_T210" "T2grad_margin_var" "T2texture_inversediffmoment_nondir"
## [9] "LMSIR" "ave_T213" "T2max_F_r_i" "T2texture_sumvariance_nondir"
## [13] "find_t2_signal_int" "T2grad_margin" "ave_T218" "ave_T217"
## [17] "LMSIR_predicted" "ave_T214" "ave_T24" "ave_T25"
## [21] "ave_T23" "T2_lesionSI" "ave_T219" "T2kurt_F_r_i"
## [25] "ave_T27" "T2_lesionSIstd" "ave_T28" "ave_T26"
## [29] "ave_T21" "T2texture_contrast_nondir" "ave_T22" "ave_T29"
## [33] "T2min_F_r_i"
## -0.03472222 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "circularity" "earlySE12" "V9" "max_F_r_i"
## [5] "texture_energy_nondir_post4" "Vr_post_1_inside" "max_RGH_mean" "texture_sumvariance_nondir_post4"
## [9] "skew_F_r_i" "V4" "V2" "A_inside"
## [13] "edge_sharp_std" "Kpeak_countor" "ivVariance" "dce3SE15"
## [17] "Slope_ini_inside" "texture_diffvariance_nondir_post4" "kurt_F_r_i" "dce2SE18"
## [21] "lateSE16" "dce3SE11" "earlySE10" "earlySE17"
## [25] "lateSE11" "texture_variance_nondir_post4" "dce2SE13" "alpha_inside"
## -0.05442177 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "irregularity" "SER_inside" "iiMin_change_Variance_uptake"
## [4] "texture_inversediffmoment_nondir_post2" "earlySE4" "texture_diffentropy_nondir_post4"
## [7] "dce3SE11" "T2texture_correlation_nondir" "edge_sharp_mean"
## [10] "min_F_r_i" "ave_T212" "T2RGH_var"
## [13] "T2texture_inversediffmoment_nondir" "ave_T27" "V6"
## [16] "Kpeak_countor" "Tpeak_inside" "V2"
## [19] "earlySE2" "dce2SE2" "earlySE6"
## [22] "V4" "texture_diffvariance_nondir_post2" "T2texture_contrast_nondir"
## [25] "earlySE14" "V8" "dce2SE0"
## [28] "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 6 6 0066 4583735 3 massB BENIGN BREAST TISSUE Hypointense or not seen
## 7 7 0066 7556910 4 nonmassB DENSE FIBROSIS None
## 13 13 0121 6714524 4 massB ADENOSIS Hypointense or not seen
## 14 14 0121 7091267 4 massB BENIGN BREAST TISSUE Hyperintense
## 18 18 0127 4696964 4 nonmassB FIBROADENOMA Hyperintense
## 20 20 0130 5017534 2 massB ATYPICAL LOBULAR HYPERPLASIA Hyperintense
## 21 21 0130 5017534 2 massB ATYPICAL LOBULAR HYPERPLASIA Hyperintense
## 22 22 0130 7347205 4 massB ATYPICAL LOBULAR HYPERPLASIA Hypointense or not seen
## 38 38 0189 5057674 4 nonmassB SCLEROSING ADENOSIS Hypointense or not seen
## 67 67 0276 6952525 4 massM InvasiveDuctal Slightly hyperintense
## 68 68 0276 6952525 4 massM InvasiveDuctal Slightly hyperintense
## 84 84 0426 7169326 4 nonmassB STROMAL FIBROSIS None
## 85 85 0426 7169326 4 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
## 86 86 0426 7169326 4 nonmassB STROMAL FIBROSIS None
## 111 111 0578 6765702 6 massM InvasiveDuctal None
## 126 126 0657 6980780 4 massM InvasiveDuctal Hypointense or not seen
## 129 129 0666 5088826 3 massM InsituDuctal Hyperintense
## 136 136 0679 4994641 6 massM InvasiveDuctal None
## 211 211 0783 4758418 3 massB FIBROCYSTIC Hyperintense
## 218 218 0789 4785741 3 massM InsituDuctal Slightly hyperintense
## 222 222 0792 5264066 3 massB DUCT PAPILLOMA Slightly hyperintense
## 223 223 0792 5264066 3 massB DUCT PAPILLOMA Slightly hyperintense
## 224 224 0793 4988020 4 massB FIBROADENOMA Hyperintense
## 225 225 0793 7135216 2 massB COMPLEX FIBROEPITHELIAL LESION Hyperintense
## 234 234 0810 4622489 4 massM InsituDuctal None
## 240 240 0815 4828432 5 massM InvasiveDuctal None
## 241 241 0817 5363917 6 massM InvasiveDuctal Hyperintense
## 271 271 0856 4986174 4 massB FIBROADENOMA Hyperintense
## 272 272 0856 4986174 4 massB FIBROADENOMA Hyperintense
## 273 273 0856 6871177 2 massB ATYPICAL DUCTAL HYPERPLASIA Hypointense or not seen
## 277 277 0862 5395314 4 massM InsituDuctal None
## 280 280 0865 5267535 5 massM InvasiveDuctal None
## 281 281 0865 5267535 5 nonmassM InvasiveDuctal None
## 308 308 0913 7350757 4 massB ADENOSIS Slightly hyperintense
## 315 315 0937 7144673 4 massB FIBROEPITHELIAL Hyperintense
## 331 331 0985 7050619 4 nonmassB COLUMNAR CELL CHANGES Hyperintense
## 335 335 0997 7279207 3 massB ATYPICAL LOBULAR HYPERPLASIA None
## 400 400 2065 7604632 4 nonmassB InsituLobular None
## 409 409 2078 5116776 4 massB BENIGN BREAST TISSUE Hyperintense
## 421 421 3018 6865137 3 massB FAT NECROSIS Hyperintense
## 427 427 3028 6991592 3 massB HYPERPLASIA Hypointense or not seen
## 434 434 3045 7149704 4 nonmassB ADENOSIS None
## 442 442 3054 6714946 4 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
## 443 443 3055 7742700 4 massB COLUMNAR CELL CHANGES Hypointense or not seen
## 444 444 3055 7060620 4 massM InvasiveDuctal Hypointense or not seen
## 445 445 3055 7742700 4 nonmassB COLUMNAR CELL CHANGES None
## 446 446 3055 7742700 4 massB STROMAL HYPERPLASIA Hypointense or not seen
## 447 447 3055 7060620 4 massM InvasiveDuctal Hypointense or not seen
## 448 448 3057 7098623 4 nonmassB BENIGN BREAST TISSUE None
## 449 449 3057 7098623 4 massB TUBULAR ADENOMA Slightly hyperintense
## 485 485 4020 6988975 6 massM InvasiveLobular Slightly hyperintense
## 497 497 4041 7003893 4 nonmassB BENIGN BREAST TISSUE Slightly hyperintense
## 553 553 6041 5104414 6 massM InvasiveDuctal Slightly hyperintense
## 554 554 6041 5104414 6 massM InvasiveDuctal None
## 562 562 6046 ACC108189 5 massM InsituDuctal Hypointense or not seen
## 563 563 6046 ACC108189 5 massM InsituDuctal Hypointense or not seen
## 564 564 6046 ACC108189 5 massM InsituDuctal Hyperintense
## 565 565 6046 ACC108189 5 massM InsituDuctal None
## 569 569 6051 5426079 6 massM InvasiveDuctal Hyperintense
## 589 589 6223 7043947 4 massM InvasiveDuctal Hyperintense
## 611 611 7085 7616788 2 massB ATYPICAL DUCTAL HYPERPLASIA None
## 614 614 7094 7171259 4 nonmassB BENIGN BREAST TISSUE None
## 617 617 7097 6805449 4 massB SCLEROSING ADENOSIS Hypointense or not seen
## 618 618 7097 6805449 4 massB FIBROADENOMA None
## 619 619 7097 7388464 2 massB ATYPICAL DUCTAL HYPERPLASIA Slightly hyperintense
## 626 626 7178 7074874 6 massM InvasiveDuctal Hypointense or not seen
## 627 627 7183 7404761 4 massB FIBROCYSTIC Hyperintense
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6779267 0.6066667
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7572563 0.5971429
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8108603 0.6009524
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8654166 0.5209524
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6779267 0.6066667
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7633993 0.5957143
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8216777 0.5838095
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8811632 0.4961905
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6779267 0.6066667
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7478875 0.6042857
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8098812 0.6
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8735715 0.6152381
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6779267 0.6066667
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7570618 0.5747619
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8070243 0.5561905
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8798822 0.522381
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6779267 0.6066667
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7636005 0.5952381
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8073327 0.5414286
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8638808 0.5385714
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6779267 0.6066667
## 2 2 25 0.7572563 0.5971429
## 3 3 25 0.8108603 0.6009524
## 4 5 25 0.8654166 0.5209524
## 5 1 20 0.6779267 0.6066667
## 6 2 20 0.7633993 0.5957143
## 7 3 20 0.8216777 0.5838095
## 8 5 20 0.8811632 0.4961905
## 9 1 15 0.6779267 0.6066667
## 10 2 15 0.7478875 0.6042857
## 11 3 15 0.8098812 0.6000000
## 12 5 15 0.8735715 0.6152381
## 13 1 10 0.6779267 0.6066667
## 14 2 10 0.7570618 0.5747619
## 15 3 10 0.8070243 0.5561905
## 16 5 10 0.8798822 0.5223810
## 17 1 5 0.6779267 0.6066667
## 18 2 5 0.7636005 0.5952381
## 19 3 5 0.8073327 0.5414286
## 20 5 5 0.8638808 0.5385714
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8735715 0.6152381
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6836002 0.617619
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7431595 0.5366667
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8330114 0.5033333
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8777697 0.5109524
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6836002 0.617619
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7519314 0.5395238
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8103774 0.5738095
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8570202 0.5057143
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6836002 0.617619
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7477332 0.6152381
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.7974341 0.5109524
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8682467 0.5614286
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6836002 0.617619
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.756988 0.5219048
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8076077 0.4914286
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8717876 0.547619
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6836002 0.617619
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7540976 0.5861905
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8071181 0.6404762
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.873082 0.5966667
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6836002 0.6176190
## 2 2 25 0.7431595 0.5366667
## 3 3 25 0.8330114 0.5033333
## 4 5 25 0.8777697 0.5109524
## 5 1 20 0.6836002 0.6176190
## 6 2 20 0.7519314 0.5395238
## 7 3 20 0.8103774 0.5738095
## 8 5 20 0.8570202 0.5057143
## 9 1 15 0.6836002 0.6176190
## 10 2 15 0.7477332 0.6152381
## 11 3 15 0.7974341 0.5109524
## 12 5 15 0.8682467 0.5614286
## 13 1 10 0.6836002 0.6176190
## 14 2 10 0.7569880 0.5219048
## 15 3 10 0.8076077 0.4914286
## 16 5 10 0.8717876 0.5476190
## 17 1 5 0.6836002 0.6176190
## 18 2 5 0.7540976 0.5861905
## 19 3 5 0.8071181 0.6404762
## 20 5 5 0.8730820 0.5966667
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8071181 0.6404762
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7480954 0.7290476
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.808721 0.64
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8477051 0.6285714
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8707683 0.62
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7480954 0.7290476
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.821054 0.6357143
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8466924 0.582381
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8890834 0.6685714
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7480954 0.7290476
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8155682 0.5880952
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8449286 0.707619
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8812906 0.6666667
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7480954 0.7290476
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8171911 0.6657143
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8401671 0.6466667
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8870111 0.402381
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7480954 0.7290476
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8245145 0.6509524
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.850106 0.6509524
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8691453 0.6004762
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7480954 0.7290476
## 2 2 25 0.8087210 0.6400000
## 3 3 25 0.8477051 0.6285714
## 4 5 25 0.8707683 0.6200000
## 5 1 20 0.7480954 0.7290476
## 6 2 20 0.8210540 0.6357143
## 7 3 20 0.8466924 0.5823810
## 8 5 20 0.8890834 0.6685714
## 9 1 15 0.7480954 0.7290476
## 10 2 15 0.8155682 0.5880952
## 11 3 15 0.8449286 0.7076190
## 12 5 15 0.8812906 0.6666667
## 13 1 10 0.7480954 0.7290476
## 14 2 10 0.8171911 0.6657143
## 15 3 10 0.8401671 0.6466667
## 16 5 10 0.8870111 0.4023810
## 17 1 5 0.7480954 0.7290476
## 18 2 5 0.8245145 0.6509524
## 19 3 5 0.8501060 0.6509524
## 20 5 5 0.8691453 0.6004762
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7480954 0.7290476
## 5 1 20 0.7480954 0.7290476
## 9 1 15 0.7480954 0.7290476
## 13 1 10 0.7480954 0.7290476
## 17 1 5 0.7480954 0.7290476
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7947851 0.7380952
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8348154 0.7652381
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8612922 0.8114286
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9006317 0.7695238
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7956771 0.7380952
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8392551 0.7395238
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8707347 0.8142857
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.9047964 0.8114286
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7947851 0.7380952
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8321195 0.7671429
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8641893 0.7966667
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9000282 0.7933333
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7947851 0.7380952
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8335211 0.7309524
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8685351 0.7485714
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8942607 0.7971429
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7947851 0.7380952
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8356001 0.7819048
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8666573 0.8147619
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9118247 0.727619
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7947851 0.7380952
## 2 2 25 0.8348154 0.7652381
## 3 3 25 0.8612922 0.8114286
## 4 5 25 0.9006317 0.7695238
## 5 1 20 0.7956771 0.7380952
## 6 2 20 0.8392551 0.7395238
## 7 3 20 0.8707347 0.8142857
## 8 5 20 0.9047964 0.8114286
## 9 1 15 0.7947851 0.7380952
## 10 2 15 0.8321195 0.7671429
## 11 3 15 0.8641893 0.7966667
## 12 5 15 0.9000282 0.7933333
## 13 1 10 0.7947851 0.7380952
## 14 2 10 0.8335211 0.7309524
## 15 3 10 0.8685351 0.7485714
## 16 5 10 0.8942607 0.7971429
## 17 1 5 0.7947851 0.7380952
## 18 2 5 0.8356001 0.7819048
## 19 3 5 0.8666573 0.8147619
## 20 5 5 0.9118247 0.7276190
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8666573 0.8147619
## id C NC pred obs
## 1 6 0.24679845 0.7532015 NC NC
## 2 7 1.03326340 -0.0332634 C NC
## 3 13 0.25151968 0.7484803 NC NC
## 4 14 0.83162600 0.1683740 C NC
## 5 18 0.19258353 0.8074165 NC NC
## 6 20 0.01868463 0.9813154 NC NC
## id C NC pred obs
## 1 6 0.9938128 0.006187184 C NC
## 2 7 0.5632899 0.436710101 C NC
## 3 13 0.4681670 0.531833030 NC NC
## 4 14 0.3721412 0.627858797 NC NC
## 5 18 0.3192681 0.680731945 NC NC
## 6 20 -0.1058656 1.105865606 NC NC
## id C NC pred obs
## 1 6 0.1641411 0.8358589 NC NC
## 2 7 0.3126478 0.6873522 NC NC
## 3 13 0.4018064 0.5981936 NC NC
## 4 14 0.2927655 0.7072345 NC NC
## 5 18 0.5892085 0.4107915 C NC
## 6 20 0.1072640 0.8927360 NC NC
## id C NC pred obs
## 1 6 0.22276604 0.7772340 NC NC
## 2 7 0.60799266 0.3920073 C NC
## 3 13 0.09454979 0.9054502 NC NC
## 4 14 0.28313819 0.7168618 NC NC
## 5 18 0.29113510 0.7088649 NC NC
## 6 20 0.16917745 0.8308225 NC NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 193 controls (perf_imgT2$obs C) > 303 cases (perf_imgT2$obs NC).
## Area under the curve: 0.6853
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 193 controls (perf_allT2$obs C) > 301 cases (perf_allT2$obs NC).
## Area under the curve: 0.7012
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 193 controls (perf_imgT1$obs C) > 303 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7375
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 193 controls (perf_all$obs C) > 303 cases (perf_all$obs NC).
## Area under the curve: 0.741
## Area under the curve: 0.6853
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3361978 0.6891 0.7513 0.8083 0.5017 0.5545 0.6073
## Area under the curve: 0.7012
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3013366 0.7927 0.8446 0.8964 0.4419 0.5017 0.5581
## Area under the curve: 0.7375
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.5907 0.658 0.7202 0.6733 0.7261 0.7756
## Area under the curve: 0.741
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3988443 0.544 0.6114 0.6788 0.7327 0.7789 0.8251
## massB massM nonmassB nonmassM
## 211 153 125 70
## massB massM nonmassB nonmassM
## 31 13 17 7
## massB massM nonmassB nonmassM
## 211 153 125 70
## massB massM nonmassB nonmassM
## 31 13 17 7
## massB massM nonmassB nonmassM
## 211 153 125 70
## massB massM nonmassB nonmassM
## 31 13 17 7
## -0.02714932 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2RGH_var" "T2RGH_mean" "T2texture_entropy_nondir" "T2grad_margin_var" "ave_T210"
## [6] "T2var_F_r_i" "ave_T21" "ave_T211" "T2skew_F_r_i" "ave_T215"
## [11] "T2texture_diffentropy_nondir" "ave_T27" "ave_T22" "ave_T28" "T2kurt_F_r_i"
## [16] "T2texture_sumvariance_nondir" "T2max_F_r_i" "T2_lesionSI" "ave_T23" "ave_T216"
## [21] "T2texture_correlation_nondir" "ave_T212" "ave_T24" "T2texture_energy_nondir" "ave_T20"
## [26] "T2texture_sumaverage_nondir" "T2min_F_r_i" "ave_T29" "ave_T25" "T2_lesionSIstd"
## 0 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_var" "ave_T210" "T2texture_correlation_nondir" "T2max_F_r_i" "T2texture_energy_nondir"
## [6] "ave_T21" "LMSIR" "ave_T28" "ave_T218" "ave_T20"
## [11] "T2_lesionSIstd" "ave_T213" "ave_T219" "T2_lesionSI" "ave_T215"
## [16] "T2grad_margin" "T2texture_diffentropy_nondir" "T2texture_variance_nondir" "T2texture_sumentropy_nondir" "T2wSI_predicted"
## [21] "ave_T214" "ave_T29" "ave_T22" "T2kurt_F_r_i" "ave_T27"
## [26] "T2grad_margin_var" "T2min_F_r_i" "ave_T216" "find_t2_signal_int"
## 0.02547771 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "texture_variance_nondir_post1" "texture_sumvariance_nondir_post1" "V9"
## [4] "Tpeak_countor" "V16" "Kpeak_inside"
## [7] "texture_inversediffmoment_nondir_post2" "texture_sumaverage_nondir_post3" "V13"
## [10] "texture_inversediffmoment_nondir_post4" "V8" "texture_correlation_nondir_post1"
## [13] "lateSE2" "UptakeRate_countor" "texture_sumvariance_nondir_post4"
## [16] "dce2SE15" "texture_diffentropy_nondir_post3" "texture_contrast_nondir_post3"
## [19] "lateSE19" "earlySE11" "lateSE1"
## [22] "earlySE3" "texture_sumaverage_nondir_post4" "earlySE0"
## [25] "dce3SE10" "min_F_r_i" "ivVariance"
## [28] "lateSE7" "dce2SE11" "Vr_post_1_countor"
## [31] "lateSE10" "skew_F_r_i" "dce2SE9"
## [34] "max_RGH_mean_k" "V6" "peakVr_inside"
## [37] "Vr_decreasingRate_countor" "iAUC1_countor" "max_RGH_var_k"
## [40] "A_inside"
## 0.1485714 0.05
## 0.1006711 0.05
## -0.05223881 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "texture_sumvariance_nondir_post1" "irregularity" "SER_inside"
## [4] "texture_inversediffmoment_nondir_post4" "texture_sumaverage_nondir_post2" "texture_diffvariance_nondir_post1"
## [7] "iiMin_change_Variance_uptake" "T2RGH_mean" "earlySE8"
## [10] "texture_contrast_nondir_post2" "V13" "V17"
## [13] "V19" "lateSE6" "dce3SE11"
## [16] "T2var_F_r_i" "Vr_increasingRate_inside" "T2kurt_F_r_i"
## [19] "LMSIR" "UptakeRate_countor" "lateSE14"
## [22] "dce2SE16" "ave_T212" "T2texture_sumentropy_nondir"
## [25] "ivVariance" "T2texture_contrast_nondir" "alpha_countor"
## [28] "T2wSI_predicted" "texture_sumaverage_nondir_post1" "dce3SE1"
## [31] "maxCr_inside" "dce2SE7" "lateSE13"
## [34] "lateSE19" "ave_T215" "max_RGH_var"
## [37] "dce3SE4" "earlySE3" "texture_entropy_nondir_post1"
## [40] "Kpeak_countor" "dce2SE10" "earlySE19"
## [43] "texture_entropy_nondir_post3" "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 4 4 0027 7171944 4 nonmassB STROMAL FIBROSIS None
## 5 5 0027 6805483 4 nonmassM InsituDuctal None
## 8 8 0093 7156466 4 nonmassM InvasiveDuctal None
## 9 9 0093 7156466 4 nonmassM InvasiveDuctal None
## 26 26 0135 7777131 4 massB FIBROCYSTIC None
## 27 27 0135 5083620 4 nonmassB FIBROCYSTIC Hypointense or not seen
## 30 30 0171 4751079 4 massM InsituDuctal Hypointense or not seen
## 31 31 0172 4703102 4 massB FIBROCYSTIC None
## 48 48 0198 4809893 2 massB FIBROCYSTIC None
## 49 49 0198 4809893 2 massB FIBROADENOMA None
## 60 60 0252 5142106 4 massB FIBROADENOMA Hypointense or not seen
## 61 61 0252 5142106 4 massB FIBROADENOMA Hypointense or not seen
## 62 62 0252 6700964 3 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
## 63 63 0252 6700964 3 massB BENIGN BREAST TISSUE Hyperintense
## 65 65 0259 7364573 2 nonmassB BENIGN BREAST TISSUE None
## 98 98 0513 5043867 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 106 106 0571 4902166 4 massM InvasiveDuctal Hypointense or not seen
## 107 107 0571 4902166 4 nonmassB DUCT PAPILLOMA Hypointense or not seen
## 120 120 0616 7910718 2 massM InsituDuctal Hypointense or not seen
## 157 157 0710 5282770 4 massB FIBROADENOMA Hyperintense
## 158 158 0710 5282770 5 massB DUCT PAPILLOMA Hyperintense
## 159 159 0710 6798490 2 massB DUCTAL HYPERPLASIA None
## 170 170 0723 4884108 6 massM InsituDuctal None
## 181 181 0734 4532660 4 massB ATYPICAL DUCTAL HYPERPLASIA Slightly hyperintense
## 248 248 0830 4863868 5 massB ATYPICAL DUCTAL HYPERPLASIA None
## 249 249 0830 4863868 5 massB Cyst None
## 261 261 0850 5380609 5 massB BENIGN BREAST TISSUE Slightly hyperintense
## 262 262 0850 5380609 5 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 263 263 0850 5380609 5 massB FIBROCYSTIC Slightly hyperintense
## 266 266 0853 4798586 2 nonmassB FIBROCYSTIC None
## 267 267 0853 4745782 3 nonmassB FIBROCYSTIC Slightly hyperintense
## 268 268 0853 6696534 4 nonmassM InsituDuctal Slightly hyperintense
## 269 269 0855 4641315 6 massB FIBROSIS Hyperintense
## 270 270 0855 4641315 6 nonmassB FIBROSIS None
## 278 278 0863 4969136 4 massB DUCT PAPILLOMA Hyperintense
## 279 279 0863 4969136 4 massM InvasiveLobular Hypointense or not seen
## 298 298 0883 5177385 5 nonmassM InsituDuctal None
## 306 306 0900 6699226 4 massB Cyst None
## 307 307 0904 7133915 3 massB FIBROCYSTIC Hyperintense
## 349 349 1027 6930730 3 nonmassB FIBROADENOMA None
## 351 351 1045 7231265 4 massB BENIGN BREAST TISSUE Hypointense or not seen
## 353 353 1026 6907382 4 massB DENSE FIBROSIS AND FIBROADENOMATOID CHANGE Hyperintense
## 354 354 1053 7748055 4 massB INFLAMED CYST WALL Hyperintense
## 358 358 1065 7741665 4 nonmassB BENIGN BREAST TISSUE None
## 375 375 1099 7646705 5 massM InsituDuctal Hypointense or not seen
## 376 376 1099 7646705 4 nonmassM InsituDuctal None
## 402 402 2069 4976319 6 massM InsituDuctal Hypointense or not seen
## 426 426 3026 6830523 4 massB FIBROCYSTIC Hypointense or not seen
## 431 431 3035 7002031 4 massB FIBROADENOMA Hyperintense
## 432 432 3035 7145247 4 massB FIBROCYSTIC None
## 438 438 3052 7100200 4 massB STROMAL FIBROSIS Hyperintense
## 439 439 3052 7100200 4 massB FIBROADENOMA Hyperintense
## 459 459 3076 7053450 6 massM InsituDuctal Hypointense or not seen
## 460 460 3076 7053450 6 massM InsituDuctal Hypointense or not seen
## 495 495 4040 7003416 6 massM InvasiveDuctal None
## 496 496 4040 7085105 4 massB FIBROADENOMA Hyperintense
## 504 504 4049 7009602 6 massM InvasiveDuctal None
## 519 519 6019 ACC109175 4 massM InvasiveLobular Hypointense or not seen
## 537 537 6032 4982490 4 nonmassB FIBROCYSTIC None
## 546 546 6038 5044471 6 massM InvasiveDuctal None
## 547 547 6038 5044471 6 nonmassB BENIGN BREAST TISSUE None
## 548 548 6038 5044471 6 nonmassB BENIGN BREAST TISSUE Hyperintense
## 581 581 6105 5069712 4 nonmassM InsituDuctal None
## 585 585 6148 7446343 4 massB SCLEROSING ADENOSIS Hypointense or not seen
## 590 590 6224 4559525 4 nonmassB FIBROCYSTIC Hyperintense
## 591 591 6226 6718391 4 massB BENIGN BREAST TISSUE Slightly hyperintense
## 603 603 7053 7956343 4 nonmassB FIBROTIC STROMA Hypointense or not seen
## 622 622 7127 6989740 4 massB BENIGN BREAST TISSUE Hypointense or not seen
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6982503 0.5286458
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.763186 0.5541667
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8017163 0.5583333
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8804119 0.5541667
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6982503 0.525
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7648676 0.4885417
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8101911 0.5348958
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8539665 0.5114583
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6982503 0.5286458
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7611107 0.515625
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.7947696 0.5307292
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8546805 0.5526042
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6982503 0.525
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7501668 0.5557292
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.7968116 0.5614583
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8613736 0.5447917
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6982503 0.5286458
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.755592 0.4921875
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8211483 0.5729167
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8634956 0.5427083
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6982503 0.5286458
## 2 2 25 0.7631860 0.5541667
## 3 3 25 0.8017163 0.5583333
## 4 5 25 0.8804119 0.5541667
## 5 1 20 0.6982503 0.5250000
## 6 2 20 0.7648676 0.4885417
## 7 3 20 0.8101911 0.5348958
## 8 5 20 0.8539665 0.5114583
## 9 1 15 0.6982503 0.5286458
## 10 2 15 0.7611107 0.5156250
## 11 3 15 0.7947696 0.5307292
## 12 5 15 0.8546805 0.5526042
## 13 1 10 0.6982503 0.5250000
## 14 2 10 0.7501668 0.5557292
## 15 3 10 0.7968116 0.5614583
## 16 5 10 0.8613736 0.5447917
## 17 1 5 0.6982503 0.5286458
## 18 2 5 0.7555920 0.4921875
## 19 3 5 0.8211483 0.5729167
## 20 5 5 0.8634956 0.5427083
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8211483 0.5729167
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6962217 0.5572917
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7513146 0.5911458
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8100777 0.5135417
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8722774 0.6395833
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6962217 0.4723958
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7562927 0.428125
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8067678 0.5682292
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8640228 0.6333333
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6962217 0.5572917
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7587084 0.49375
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8164905 0.5026042
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8800649 0.5510417
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6962217 0.4770833
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7608638 0.5276042
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8180787 0.5354167
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8633021 0.4869792
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6962217 0.4723958
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7503136 0.5463542
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8059671 0.5234375
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8639027 0.5901042
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6962217 0.5572917
## 2 2 25 0.7513146 0.5911458
## 3 3 25 0.8100777 0.5135417
## 4 5 25 0.8722774 0.6395833
## 5 1 20 0.6962217 0.4723958
## 6 2 20 0.7562927 0.4281250
## 7 3 20 0.8067678 0.5682292
## 8 5 20 0.8640228 0.6333333
## 9 1 15 0.6962217 0.5572917
## 10 2 15 0.7587084 0.4937500
## 11 3 15 0.8164905 0.5026042
## 12 5 15 0.8800649 0.5510417
## 13 1 10 0.6962217 0.4770833
## 14 2 10 0.7608638 0.5276042
## 15 3 10 0.8180787 0.5354167
## 16 5 10 0.8633021 0.4869792
## 17 1 5 0.6962217 0.4723958
## 18 2 5 0.7503136 0.5463542
## 19 3 5 0.8059671 0.5234375
## 20 5 5 0.8639027 0.5901042
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8722774 0.6395833
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7647075 0.6432292
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8212684 0.6098958
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8772221 0.6416667
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8981956 0.6552083
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7647075 0.6432292
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8262799 0.5973958
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.870182 0.6484375
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8971212 0.6723958
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7547846 0.3807292
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.815236 0.6135417
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8774891 0.6734375
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.891636 0.6432292
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7639467 0.6239583
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8254257 0.5958333
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8636691 0.6447917
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9062033 0.6395833
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7647075 0.6432292
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8271474 0.56875
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.881286 0.6432292
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9052157 0.696875
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7647075 0.6432292
## 2 2 25 0.8212684 0.6098958
## 3 3 25 0.8772221 0.6416667
## 4 5 25 0.8981956 0.6552083
## 5 1 20 0.7647075 0.6432292
## 6 2 20 0.8262799 0.5973958
## 7 3 20 0.8701820 0.6484375
## 8 5 20 0.8971212 0.6723958
## 9 1 15 0.7547846 0.3807292
## 10 2 15 0.8152360 0.6135417
## 11 3 15 0.8774891 0.6734375
## 12 5 15 0.8916360 0.6432292
## 13 1 10 0.7639467 0.6239583
## 14 2 10 0.8254257 0.5958333
## 15 3 10 0.8636691 0.6447917
## 16 5 10 0.9062033 0.6395833
## 17 1 5 0.7647075 0.6432292
## 18 2 5 0.8271474 0.5687500
## 19 3 5 0.8812860 0.6432292
## 20 5 5 0.9052157 0.6968750
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9052157 0.696875
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.8074418 0.7796875
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8551943 0.6942708
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8981422 0.6989583
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9344904 0.684375
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.8071749 0.7729167
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8500561 0.6953125
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8814262 0.7052083
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.9158792 0.75
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.8070414 0.7817708
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8573631 0.7505208
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8879524 0.715625
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9238069 0.690625
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.8071749 0.7682292
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8584308 0.7651042
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8917494 0.6927083
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9265094 0.6895833
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.8067211 0.7723958
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8616605 0.7114583
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8848294 0.7322917
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9200499 0.7083333
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.8074418 0.7796875
## 2 2 25 0.8551943 0.6942708
## 3 3 25 0.8981422 0.6989583
## 4 5 25 0.9344904 0.6843750
## 5 1 20 0.8071749 0.7729167
## 6 2 20 0.8500561 0.6953125
## 7 3 20 0.8814262 0.7052083
## 8 5 20 0.9158792 0.7500000
## 9 1 15 0.8070414 0.7817708
## 10 2 15 0.8573631 0.7505208
## 11 3 15 0.8879524 0.7156250
## 12 5 15 0.9238069 0.6906250
## 13 1 10 0.8071749 0.7682292
## 14 2 10 0.8584308 0.7651042
## 15 3 10 0.8917494 0.6927083
## 16 5 10 0.9265094 0.6895833
## 17 1 5 0.8067211 0.7723958
## 18 2 5 0.8616605 0.7114583
## 19 3 5 0.8848294 0.7322917
## 20 5 5 0.9200499 0.7083333
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.8070414 0.7817708
## id C NC pred obs
## 1 4 0.86186952 0.1381305 C NC
## 2 5 0.61074027 0.3892597 C C
## 3 8 0.52422918 0.4757708 C C
## 4 9 0.30006338 0.6999366 NC C
## 5 26 -0.03469911 1.0346991 NC NC
## 6 27 0.61074027 0.3892597 C NC
## id C NC pred obs
## 1 4 0.8238381 0.1761619 C NC
## 2 5 0.7950526 0.2049474 C C
## 3 8 0.3790880 0.6209120 NC C
## 4 9 0.3738235 0.6261765 NC C
## 5 26 -0.1177962 1.1177962 NC NC
## 6 27 0.5866793 0.4133207 C NC
## id C NC pred obs
## 1 4 0.5462902 0.4537098 C NC
## 2 5 0.5138468 0.4861532 C C
## 3 8 0.5016440 0.4983560 C C
## 4 9 0.4224391 0.5775609 NC C
## 5 26 0.4172334 0.5827666 NC NC
## 6 27 0.2018588 0.7981412 NC NC
## id C NC pred obs
## 1 4 0.2591745 0.7408255 NC NC
## 2 5 0.2922313 0.7077687 NC C
## 3 8 0.4960581 0.5039419 NC C
## 4 9 0.6557460 0.3442540 C C
## 5 26 0.3033432 0.6966568 NC NC
## 6 27 0.4753663 0.5246337 NC NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 213 controls (perf_imgT2$obs C) > 351 cases (perf_imgT2$obs NC).
## Area under the curve: 0.6679
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 213 controls (perf_allT2$obs C) > 349 cases (perf_allT2$obs NC).
## Area under the curve: 0.6892
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 213 controls (perf_imgT1$obs C) > 351 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7324
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 213 controls (perf_all$obs C) > 351 cases (perf_all$obs NC).
## Area under the curve: 0.7425
## Area under the curve: 0.6679
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3361978 0.69 0.7465 0.8028 0.4701 0.5242 0.5755
## Area under the curve: 0.6892
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3013366 0.7887 0.8404 0.8873 0.4327 0.4871 0.5415
## Area under the curve: 0.7324
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.5961 0.6573 0.7183 0.6638 0.7123 0.7607
## Area under the curve: 0.7425
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3979641 0.554 0.6197 0.6854 0.7293 0.7721 0.8148
## massB massM nonmassB nonmassM
## 220 149 131 64
## massB massM nonmassB nonmassM
## 22 17 11 13
## massB massM nonmassB nonmassM
## 220 149 131 64
## massB massM nonmassB nonmassM
## 22 17 11 13
## massB massM nonmassB nonmassM
## 220 149 131 64
## massB massM nonmassB nonmassM
## 22 17 11 13
## 0.0361991 0.05
## Selected features for group: MeanDecreaseGini imgT2
## =========NULL
## [1] "T2texture_correlation_nondir" "T2texture_entropy_nondir" "T2RGH_var" "T2RGH_mean"
## [5] "T2skew_F_r_i" "T2var_F_r_i" "ave_T20" "ave_T28"
## [9] "T2texture_sumaverage_nondir" "T2grad_margin_var" "ave_T215" "ave_T218"
## [13] "T2texture_contrast_nondir" "ave_T27" "ave_T25" "ave_T24"
## [17] "ave_T26" "ave_T213" "ave_T214" "T2texture_variance_nondir"
## [21] "T2grad_margin" "T2kurt_F_r_i" "ave_T211" "ave_T210"
## [25] "ave_T212" "T2_lesionSI" "ave_T219" "T2min_F_r_i"
## [29] "T2texture_sumentropy_nondir" "T2texture_inversediffmoment_nondir" "ave_T29" "T2texture_sumvariance_nondir"
## [33] "ave_T217" "ave_T216" "T2_lesionSIstd"
## 0.06578947 0.05
## 0.0657277 0.05
## -0.05527638 0.05
## Selected features for group: MeanDecreaseGini allT2
## =========NULL
## [1] "T2RGH_var" "ave_T210" "T2texture_correlation_nondir" "T2kurt_F_r_i"
## [5] "T2texture_entropy_nondir" "find_t2_signal_int" "LMSIR" "T2texture_inversediffmoment_nondir"
## [9] "T2grad_margin_var" "LMSIR_predicted" "ave_T27" "ave_T25"
## [13] "ave_T212" "T2texture_sumaverage_nondir" "T2texture_contrast_nondir" "T2skew_F_r_i"
## [17] "ave_T216" "ave_T219" "ave_T211" "T2_lesionSI"
## [21] "ave_T22" "ave_T217" "ave_T218" "T2RGH_mean"
## [25] "ave_T214" "ave_T215" "ave_T26" "ave_T20"
## [29] "T2max_F_r_i" "T2min_F_r_i" "ave_T29" "ave_T24"
## [33] "T2var_F_r_i" "ave_T213" "ave_T21" "T2texture_diffvariance_nondir"
## [37] "ave_T23" "T2texture_sumentropy_nondir" "T2texture_diffentropy_nondir" "T2_lesionSIstd"
## -0.06493506 0.05
## Selected features for group: MeanDecreaseGini imgT1
## =========NULL
## [1] "irregularity" "SER_inside" "texture_contrast_nondir_post1"
## [4] "texture_inversediffmoment_nondir_post2" "SER_countor" "dce2SE8"
## [7] "texture_correlation_nondir_post4" "max_RGH_mean" "texture_inversediffmoment_nondir_post1"
## [10] "texture_contrast_nondir_post3" "Tpeak_inside" "iAUC1_countor"
## [13] "edge_sharp_std" "dce3SE4" "dce3SE17"
## [16] "V7" "lateSE19" "beta_countor"
## [19] "V9" "dce2SE5" "texture_sumentropy_nondir_post2"
## [22] "V6" "V10" "dce3SE15"
## [25] "Tpeak_countor" "A_inside"
## 0.03225806 0.05
## Selected features for group: MeanDecreaseGini all
## =========NULL
## [1] "texture_variance_nondir_post1" "texture_energy_nondir_post4" "V10" "V5"
## [5] "iiiMax_Margin_Gradient" "T2RGH_mean" "maxCr_countor" "var_F_r_i"
## [9] "texture_correlation_nondir_post2" "texture_sumaverage_nondir_post2" "texture_sumentropy_nondir_post3" "texture_sumaverage_nondir_post4"
## [13] "ave_T210" "T2texture_sumvariance_nondir" "T2grad_margin_var" "dce3SE11"
## [17] "T2texture_sumaverage_nondir" "texture_entropy_nondir_post2" "dce2SE17" "kurt_F_r_i"
## [21] "washoutRate_countor" "V3" "find_t2_signal_int" "max_RGH_var"
## [25] "lateSE8" "lateSE17" "earlySE3" "V14"
## [29] "ave_T217" "ave_T25" "k_Max_Margin_Grad" "V16"
## [33] "A_inside"
## lesion_id cad_pt_no_txt exam_a_number_txt BIRADS lesion_label lesion_diagnosis find_t2_signal_int
## 2 2 0016 6920252 4 massB FLORID DUCT HYPERPLASIA Slightly hyperintense
## 19 19 0129 5326737 4 massB BENIGN BREAST TISSUE Hyperintense
## 25 25 0133 7072006 4 massB FIBROCYSTIC Hypointense or not seen
## 29 29 0168 5240535 4 massB FIBROCYSTIC None
## 37 37 0186 6869828 4 nonmassM InsituDuctal None
## 53 53 0212 4734525 4 massB FIBROADENOMA Hyperintense
## 56 56 0229 6831376 5 nonmassB FIBROCYSTIC None
## 59 59 0246 7485590 4 massB BENIGN BREAST TISSUE Hyperintense
## 140 140 0684 5266209 4 nonmassM InsituDuctal None
## 141 141 0685 5456684 4 massB FIBROCYSTIC None
## 151 151 0692 5199366 4 massB FIBROADENOMA Hypointense or not seen
## 160 160 0713 5150291 5 massM InvasiveDuctal None
## 161 161 0713 5150291 5 nonmassM InvasiveDuctal None
## 197 197 0757 4779344 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA Hyperintense
## 201 201 0765 5094113 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 220 220 0791 5365218 5 massM InvasiveLobular None
## 221 221 0791 5365218 5 nonmassM InvasiveLobular None
## 231 231 0805 5059167 4 nonmassB FIBROCYSTIC None
## 238 238 0814 4704240 5 massM InvasiveDuctal None
## 239 239 0814 6667547 4 nonmassB ATYPICAL DUCTAL HYPERPLASIA None
## 259 259 0846 4800867 5 massM MetaplasticCarcinoma Hypointense or not seen
## 264 264 0851 4593282 4 massB InsituLobular Hyperintense
## 265 265 0851 4593282 4 massM InvasiveDuctal Hyperintense
## 310 310 0920 7095635 4 massB FIBROADENOMA Hypointense or not seen
## 312 312 0924 7532614 4 massB ADENOSIS Hyperintense
## 313 313 0924 7532614 4 massB ADENOSIS Hypointense or not seen
## 314 314 0934 5314924 4 nonmassB FIBROADENOMA None
## 330 330 0978 4851428 4 nonmassB FIBROCYSTIC None
## 336 336 0999 6925971 3 massB FIBROADENOMA Slightly hyperintense
## 337 337 1003 6682777 4 nonmassM InvasiveDuctal Slightly hyperintense
## 344 344 1018 4773924 4 nonmassB BENIGN BREAST TISSUE Hypointense or not seen
## 392 392 2049 5458850 5 nonmassM InvasiveDuctal Hypointense or not seen
## 393 393 2049 5458850 5 massM InvasiveDuctal Hypointense or not seen
## 405 405 2073 4745825 5 massM InvasiveDuctal micropapillary None
## 406 406 2073 4745825 5 nonmassM InvasiveLobular None
## 410 410 2079 4591198 3 massB benign lymphoid tissue None
## 440 440 3053 7041483 6 massB COLUMNAR CELL CHANGES Hypointense or not seen
## 441 441 3053 7449310 5 nonmassM InvasiveDuctal None
## 450 450 3063 7053508 6 nonmassM LYMPHOVASCULAR INVASION None
## 464 464 3080 7033654 6 nonmassM InsituDuctal Hypointense or not seen
## 467 467 3082 5355166 6 massB FIBROADENOMA None
## 468 468 3082 5355166 6 massB FIBROCYSTIC None
## 469 469 3082 7080675 4 nonmassB FIBROCYSTIC None
## 512 512 6008 4644038 6 massM InvasiveDuctal Hypointense or not seen
## 520 520 6020 ACC109177 6 massM InvasiveDuctal Hypointense or not seen
## 522 522 6022 5046558 4 nonmassB FIBROADENOMA None
## 523 523 6022 5046558 6 massM InvasiveDuctal None
## 526 526 6024 5008021 5 massM InvasiveDuctal None
## 527 527 6024 5008021 5 nonmassM InvasiveDuctal None
## 528 528 6025 5111910 6 massM InvasiveDuctal Hyperintense
## 529 529 6025 5111910 6 massM InvasiveDuctal Slightly hyperintense
## 530 530 6025 5111910 6 nonmassM InvasiveDuctal None
## 568 568 6050 5225817 4 nonmassB FIBROSIS Hypointense or not seen
## 594 594 7011 6918051 4 massB BENIGN BREAST TISSUE Hypointense or not seen
## 595 595 7018 6803089 4 massM InsituDuctal None
## 596 596 7018 7138226 2 massM InsituDuctal None
## 599 599 7030 7538617 4 massB BENIGN BREAST TISSUE Slightly hyperintense
## 600 600 7030 7538617 4 massB BENIGN BREAST TISSUE Hypointense or not seen
## 608 608 7077 5077480 5 massM InsituDuctal None
## 609 609 7077 5077480 5 massM InsituDuctal None
## 610 610 7077 5077480 5 nonmassM InsituDuctal None
## 629 629 7189 7068978 4 massB FIBROADENOMA Hyperintense
## 630 630 7189 7068978 4 massB BENIGN BREAST TISSUE Hyperintense
##
## ============ bagging trees treedata_imgT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6701042 0.6767677
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.749368 0.6828283
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8057729 0.6611111
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8482605 0.6272727
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6701042 0.6767677
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7435496 0.6666667
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.7950457 0.6469697
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8735203 0.5631313
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6701042 0.6767677
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7445595 0.7065657
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8199176 0.6232323
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8512165 0.6151515
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6701042 0.6767677
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7487527 0.6954545
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8098458 0.6939394
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8571553 0.7020202
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6701042 0.6767677
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7580153 0.7035354
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.7993459 0.6626263
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8595428 0.6606061
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6701042 0.6767677
## 2 2 25 0.7493680 0.6828283
## 3 3 25 0.8057729 0.6611111
## 4 5 25 0.8482605 0.6272727
## 5 1 20 0.6701042 0.6767677
## 6 2 20 0.7435496 0.6666667
## 7 3 20 0.7950457 0.6469697
## 8 5 20 0.8735203 0.5631313
## 9 1 15 0.6701042 0.6767677
## 10 2 15 0.7445595 0.7065657
## 11 3 15 0.8199176 0.6232323
## 12 5 15 0.8512165 0.6151515
## 13 1 10 0.6701042 0.6767677
## 14 2 10 0.7487527 0.6954545
## 15 3 10 0.8098458 0.6939394
## 16 5 10 0.8571553 0.7020202
## 17 1 5 0.6701042 0.6767677
## 18 2 5 0.7580153 0.7035354
## 19 3 5 0.7993459 0.6626263
## 20 5 5 0.8595428 0.6606061
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7445595 0.7065657
##
## ============ bagging trees treedata_allT2
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6866431 0.6828283
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.7554004 0.6489899
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8090767 0.629798
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.8814788 0.5833333
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.6866431 0.6828283
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.7467397 0.629798
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.7997673 0.6888889
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8684242 0.6085859
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.6866431 0.6828283
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.7452216 0.6646465
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8107954 0.6409091
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8633749 0.6186869
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.6866431 0.6828283
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.7517555 0.689899
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.7966708 0.5984848
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.8757607 0.629798
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.6866431 0.6828283
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7546514 0.7176768
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.816139 0.6035354
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8620708 0.5979798
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.6866431 0.6828283
## 2 2 25 0.7554004 0.6489899
## 3 3 25 0.8090767 0.6297980
## 4 5 25 0.8814788 0.5833333
## 5 1 20 0.6866431 0.6828283
## 6 2 20 0.7467397 0.6297980
## 7 3 20 0.7997673 0.6888889
## 8 5 20 0.8684242 0.6085859
## 9 1 15 0.6866431 0.6828283
## 10 2 15 0.7452216 0.6646465
## 11 3 15 0.8107954 0.6409091
## 12 5 15 0.8633749 0.6186869
## 13 1 10 0.6866431 0.6828283
## 14 2 10 0.7517555 0.6898990
## 15 3 10 0.7966708 0.5984848
## 16 5 10 0.8757607 0.6297980
## 17 1 5 0.6866431 0.6828283
## 18 2 5 0.7546514 0.7176768
## 19 3 5 0.8161390 0.6035354
## 20 5 5 0.8620708 0.5979798
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.7546514 0.7176768
##
## ============ bagging trees treedata_imgT1
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.79641 0.8959596
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8327983 0.909596
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.864766 0.9065657
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9015288 0.8767677
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.79641 0.8959596
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8332999 0.9146465
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8593957 0.9136364
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.8952691 0.8823232
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.79641 0.8959596
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8317416 0.9070707
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8680965 0.8944444
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.8902599 0.8964646
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.79641 0.8959596
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8374731 0.9015152
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8685981 0.9065657
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.898526 0.8883838
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.79641 0.8959596
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8375065 0.9126263
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.8634284 0.890404
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.8933497 0.8893939
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7964100 0.8959596
## 2 2 25 0.8327983 0.9095960
## 3 3 25 0.8647660 0.9065657
## 4 5 25 0.9015288 0.8767677
## 5 1 20 0.7964100 0.8959596
## 6 2 20 0.8332999 0.9146465
## 7 3 20 0.8593957 0.9136364
## 8 5 20 0.8952691 0.8823232
## 9 1 15 0.7964100 0.8959596
## 10 2 15 0.8317416 0.9070707
## 11 3 15 0.8680965 0.8944444
## 12 5 15 0.8902599 0.8964646
## 13 1 10 0.7964100 0.8959596
## 14 2 10 0.8374731 0.9015152
## 15 3 10 0.8685981 0.9065657
## 16 5 10 0.8985260 0.8883838
## 17 1 5 0.7964100 0.8959596
## 18 2 5 0.8375065 0.9126263
## 19 3 5 0.8634284 0.8904040
## 20 5 5 0.8933497 0.8893939
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8332999 0.9146465
##
## ============ bagging trees treedata_all
## maxinter: 1 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7603761 0.8151515
## maxinter: 2 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 2 2 25 0.8214625 0.7656566
## maxinter: 3 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 3 3 25 0.8837527 0.8136364
## maxinter: 5 nodesize: 25
## maxinter nodesize rocTrain rocTest
## 4 5 25 0.9081966 0.8176768
## maxinter: 1 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 5 1 20 0.7603761 0.8151515
## maxinter: 2 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 6 2 20 0.8214424 0.7575758
## maxinter: 3 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 7 3 20 0.8647459 0.7969697
## maxinter: 5 nodesize: 20
## maxinter nodesize rocTrain rocTest
## 8 5 20 0.9091529 0.8116162
## maxinter: 1 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 9 1 15 0.7603761 0.8151515
## maxinter: 2 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 10 2 15 0.8212685 0.7934343
## maxinter: 3 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 11 3 15 0.8699959 0.7282828
## maxinter: 5 nodesize: 15
## maxinter nodesize rocTrain rocTest
## 12 5 15 0.9089122 0.7434343
## maxinter: 1 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 13 1 10 0.7618474 0.8151515
## maxinter: 2 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 14 2 10 0.8174966 0.780303
## maxinter: 3 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 15 3 10 0.8713602 0.7560606
## maxinter: 5 nodesize: 10
## maxinter nodesize rocTrain rocTest
## 16 5 10 0.9041504 0.8242424
## maxinter: 1 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 17 1 5 0.7603761 0.8151515
## maxinter: 2 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 18 2 5 0.8264583 0.7631313
## maxinter: 3 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.870163 0.8313131
## maxinter: 5 nodesize: 5
## maxinter nodesize rocTrain rocTest
## 20 5 5 0.9110322 0.8116162
## maxinter nodesize rocTrain rocTest
## 1 1 25 0.7603761 0.8151515
## 2 2 25 0.8214625 0.7656566
## 3 3 25 0.8837527 0.8136364
## 4 5 25 0.9081966 0.8176768
## 5 1 20 0.7603761 0.8151515
## 6 2 20 0.8214424 0.7575758
## 7 3 20 0.8647459 0.7969697
## 8 5 20 0.9091529 0.8116162
## 9 1 15 0.7603761 0.8151515
## 10 2 15 0.8212685 0.7934343
## 11 3 15 0.8699959 0.7282828
## 12 5 15 0.9089122 0.7434343
## 13 1 10 0.7618474 0.8151515
## 14 2 10 0.8174966 0.7803030
## 15 3 10 0.8713602 0.7560606
## 16 5 10 0.9041504 0.8242424
## 17 1 5 0.7603761 0.8151515
## 18 2 5 0.8264583 0.7631313
## 19 3 5 0.8701630 0.8313131
## 20 5 5 0.9110322 0.8116162
## maxinter nodesize rocTrain rocTest
## 19 3 5 0.870163 0.8313131
## id C NC pred obs
## 1 2 0.1694571 0.8305429 NC NC
## 2 19 0.5982559 0.4017441 C NC
## 3 25 0.1106328 0.8893672 NC NC
## 4 29 0.4432475 0.5567525 NC NC
## 5 37 0.4592908 0.5407092 NC C
## 6 53 0.1723497 0.8276503 NC NC
## id C NC pred obs
## 1 2 0.2765442 0.7234558 NC NC
## 2 19 0.5686091 0.4313909 C NC
## 3 25 0.3509509 0.6490491 NC NC
## 4 29 0.3627689 0.6372311 NC NC
## 5 37 0.4058001 0.5941999 NC C
## 6 53 -0.2189842 1.2189842 NC NC
## id C NC pred obs
## 1 2 0.06613171 0.9338683 NC NC
## 2 19 0.23147894 0.7685211 NC NC
## 3 25 0.27778467 0.7222153 NC NC
## 4 29 0.06613171 0.9338683 NC NC
## 5 37 0.43074382 0.5692562 NC C
## 6 53 0.10056478 0.8994352 NC NC
## id C NC pred obs
## 1 2 0.13856303 0.8614370 NC NC
## 2 19 0.14500640 0.8549936 NC NC
## 3 25 0.32807330 0.6719267 NC NC
## 4 29 0.01666631 0.9833337 NC NC
## 5 37 0.36842978 0.6315702 NC C
## 6 53 0.23504856 0.7649514 NC NC
##
## Call:
## roc.default(response = perf_imgT2$obs, predictor = perf_imgT2$C)
##
## Data: perf_imgT2$C in 243 controls (perf_imgT2$obs C) > 384 cases (perf_imgT2$obs NC).
## Area under the curve: 0.6689
##
## Call:
## roc.default(response = perf_allT2$obs, predictor = perf_allT2$C)
##
## Data: perf_allT2$C in 243 controls (perf_allT2$obs C) > 382 cases (perf_allT2$obs NC).
## Area under the curve: 0.6894
##
## Call:
## roc.default(response = perf_imgT1$obs, predictor = perf_imgT1$C)
##
## Data: perf_imgT1$C in 243 controls (perf_imgT1$obs C) > 384 cases (perf_imgT1$obs NC).
## Area under the curve: 0.7544
##
## Call:
## roc.default(response = perf_all$obs, predictor = perf_all$C)
##
## Data: perf_all$C in 243 controls (perf_all$obs C) > 384 cases (perf_all$obs NC).
## Area under the curve: 0.7481
## Area under the curve: 0.6689
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.4328689 0.535 0.5967 0.6584 0.6276 0.6771 0.724
## Area under the curve: 0.6894
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3013366 0.7901 0.8395 0.8848 0.445 0.4895 0.5419
## Area under the curve: 0.7544
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.6255 0.6831 0.7449 0.6797 0.7266 0.7708
## Area under the curve: 0.7481
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3979641 0.5391 0.6008 0.6584 0.7396 0.7839 0.8256
plot results
print(summary(cvauc_imgT2))
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.5729 0.6565 0.6988 0.6858 0.7209 0.7641
print(summary(cvauc_allT2))
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.6262 0.6465 0.6947 0.7010 0.7233 0.8464
print(summary(cvauc_imgT1))
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.6967 0.7092 0.7500 0.7611 0.7890 0.9146
print(summary(cvauc_all))
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.6799 0.7087 0.7591 0.7569 0.8054 0.8313
# plot features
## group with all of the features spaces combined, most contributing T2w feature
## imgT2featsel ###########
# pick frequency of 75% or higher as very common feature
require(ggplot2)
dfimgT2 = data.frame(table(imgT2featsel$selfeat))
dfimgT2$high = (dfimgT2$Freq>=0.75*max(imgT2featsel$lop))*1
print(dfimgT2[dfimgT2$high==1, ])
## Var1 Freq high
## 1 ave_T20 10 1
## 2 ave_T21 7 1
## 3 ave_T210 10 1
## 4 ave_T211 9 1
## 5 ave_T212 8 1
## 6 ave_T213 8 1
## 7 ave_T214 7 1
## 8 ave_T215 10 1
## 9 ave_T216 9 1
## 10 ave_T217 8 1
## 11 ave_T218 5 1
## 12 ave_T219 8 1
## 13 ave_T22 8 1
## 14 ave_T23 6 1
## 15 ave_T24 10 1
## 16 ave_T25 9 1
## 17 ave_T26 8 1
## 18 ave_T27 8 1
## 19 ave_T28 9 1
## 20 ave_T29 9 1
## 21 T2_lesionSI 10 1
## 22 T2_lesionSIstd 8 1
## 23 T2grad_margin 5 1
## 24 T2grad_margin_var 8 1
## 25 T2kurt_F_r_i 10 1
## 26 T2max_F_r_i 7 1
## 27 T2mean_F_r_i 3 1
## 28 T2min_F_r_i 9 1
## 29 T2RGH_mean 9 1
## 30 T2RGH_var 10 1
## 31 T2skew_F_r_i 8 1
## 32 T2texture_contrast_nondir 4 1
## 33 T2texture_correlation_nondir 10 1
## 34 T2texture_diffentropy_nondir 5 1
## 35 T2texture_diffvariance_nondir 4 1
## 36 T2texture_energy_nondir 8 1
## 37 T2texture_entropy_nondir 7 1
## 38 T2texture_inversediffmoment_nondir 9 1
## 39 T2texture_sumaverage_nondir 8 1
## 40 T2texture_sumentropy_nondir 7 1
## 41 T2texture_sumvariance_nondir 8 1
## 42 T2texture_variance_nondir 4 1
## 43 T2var_F_r_i 7 1
#qplot(factor(selfeat), data=imgT2featsel, geom="bar", fill=factor(high))
ggplot(dfimgT2, aes(x=Var1, y=Freq, fill=factor(high))) +
geom_bar(stat = "identity") + coord_flip() +
ggtitle("imgT2featsel") +
labs(y="featsel frequency", x=" ") +
theme(plot.title = element_text(family = "Trebuchet MS", color="#666666", face="bold", size=22, hjust=0))+
theme(axis.title = element_text(family = "Trebuchet MS", color="#666666", face="bold", size=16))
## allT2featsel ###########
# pick frequency of 75% or higher as very common feature
dfallT2 = data.frame(table(allT2featsel$selfeat))
dfallT2$high = (dfallT2$Freq>=0.75*max(allT2featsel$lop))*1
print(dfallT2[dfallT2$high==1, ])
## Var1 Freq high
## 1 ave_T20 8 1
## 2 ave_T21 8 1
## 3 ave_T210 10 1
## 4 ave_T211 7 1
## 5 ave_T212 3 1
## 6 ave_T213 8 1
## 7 ave_T214 9 1
## 8 ave_T215 8 1
## 9 ave_T216 8 1
## 10 ave_T217 8 1
## 11 ave_T218 9 1
## 12 ave_T219 8 1
## 13 ave_T22 9 1
## 14 ave_T23 6 1
## 15 ave_T24 8 1
## 16 ave_T25 9 1
## 17 ave_T26 5 1
## 18 ave_T27 7 1
## 19 ave_T28 7 1
## 20 ave_T29 9 1
## 21 find_t2_signal_int 10 1
## 22 LMSIR 10 1
## 23 LMSIR_predicted 8 1
## 24 T2_lesionSI 9 1
## 25 T2_lesionSIstd 9 1
## 26 T2grad_margin 6 1
## 27 T2grad_margin_var 9 1
## 28 T2kurt_F_r_i 10 1
## 29 T2max_F_r_i 9 1
## 30 T2mean_F_r_i 2 1
## 31 T2min_F_r_i 7 1
## 32 T2RGH_mean 7 1
## 33 T2RGH_var 9 1
## 34 T2skew_F_r_i 7 1
## 35 T2texture_contrast_nondir 5 1
## 36 T2texture_correlation_nondir 10 1
## 37 T2texture_diffentropy_nondir 5 1
## 38 T2texture_diffvariance_nondir 5 1
## 39 T2texture_energy_nondir 8 1
## 40 T2texture_entropy_nondir 5 1
## 41 T2texture_inversediffmoment_nondir 6 1
## 42 T2texture_sumaverage_nondir 7 1
## 43 T2texture_sumentropy_nondir 4 1
## 44 T2texture_sumvariance_nondir 5 1
## 45 T2texture_variance_nondir 2 1
## 46 T2var_F_r_i 3 1
## 47 T2wSI_predicted 4 1
#qplot(factor(selfeat), data=allT2featsel, geom="bar", fill=factor(high))
ggplot(dfallT2, aes(x=Var1, y=Freq, fill=factor(high))) +
geom_bar(stat = "identity") + coord_flip() +
ggtitle("allT2featsel") +
labs(y="featsel frequency", x=" ") +
theme(plot.title = element_text(family = "Trebuchet MS", color="#666666", face="bold", size=22, hjust=0))+
theme(axis.title = element_text(family = "Trebuchet MS", color="#666666", face="bold", size=16))
## imgT1featsel ###########
# pick frequency of 75% or higher as very common feature
dfimgT1 = data.frame(table(imgT1featsel$selfeat))
dfimgT1$high = (dfimgT1$Freq>=0.75*max(imgT1featsel$lop))*1
print(dfimgT1[dfimgT1$high==1, ])
## Var1 Freq high
## 1 A_countor 2 1
## 2 A_inside 10 1
## 3 alpha_countor 2 1
## 4 alpha_inside 4 1
## 5 beta_countor 1 1
## 6 beta_inside 2 1
## 7 circularity 4 1
## 8 dce2SE0 2 1
## 9 dce2SE1 1 1
## 10 dce2SE11 4 1
## 11 dce2SE12 1 1
## 12 dce2SE13 2 1
## 13 dce2SE14 1 1
## 14 dce2SE15 2 1
## 15 dce2SE16 3 1
## 16 dce2SE17 1 1
## 17 dce2SE18 2 1
## 18 dce2SE4 1 1
## 19 dce2SE5 1 1
## 20 dce2SE7 4 1
## 21 dce2SE8 2 1
## 22 dce2SE9 1 1
## 23 dce3SE0 1 1
## 24 dce3SE10 3 1
## 25 dce3SE11 2 1
## 26 dce3SE13 2 1
## 27 dce3SE15 2 1
## 28 dce3SE16 1 1
## 29 dce3SE17 3 1
## 30 dce3SE18 1 1
## 31 dce3SE4 1 1
## 32 dce3SE5 2 1
## 33 dce3SE6 1 1
## 34 dce3SE7 1 1
## 35 dce3SE8 1 1
## 36 earlySE0 1 1
## 37 earlySE1 1 1
## 38 earlySE10 2 1
## 39 earlySE11 2 1
## 40 earlySE12 3 1
## 41 earlySE13 1 1
## 42 earlySE15 1 1
## 43 earlySE16 2 1
## 44 earlySE17 1 1
## 45 earlySE18 1 1
## 46 earlySE19 2 1
## 47 earlySE2 2 1
## 48 earlySE3 1 1
## 49 earlySE4 1 1
## 50 earlySE5 1 1
## 51 earlySE7 2 1
## 52 earlySE8 1 1
## 53 earlySE9 1 1
## 54 edge_sharp_mean 1 1
## 55 edge_sharp_std 6 1
## 56 iAUC1_countor 2 1
## 57 iiiMax_Margin_Gradient 1 1
## 58 iiMin_change_Variance_uptake 3 1
## 59 iMax_Variance_uptake 2 1
## 60 irregularity 3 1
## 61 ivVariance 4 1
## 62 Kpeak_countor 1 1
## 63 Kpeak_inside 3 1
## 64 kurt_F_r_i 5 1
## 65 lateSE0 2 1
## 66 lateSE1 3 1
## 67 lateSE10 1 1
## 68 lateSE11 2 1
## 69 lateSE12 2 1
## 70 lateSE13 1 1
## 71 lateSE14 1 1
## 72 lateSE16 2 1
## 73 lateSE18 1 1
## 74 lateSE19 3 1
## 75 lateSE2 2 1
## 76 lateSE3 1 1
## 77 lateSE4 2 1
## 78 lateSE5 2 1
## 79 lateSE6 1 1
## 80 lateSE7 2 1
## 81 lateSE8 1 1
## 82 lateSE9 2 1
## 83 max_F_r_i 2 1
## 84 max_RGH_mean 3 1
## 85 max_RGH_mean_k 2 1
## 86 max_RGH_var 1 1
## 87 max_RGH_var_k 3 1
## 88 maxCr_inside 2 1
## 89 maxVr_countor 2 1
## 90 mean_F_r_i 1 1
## 91 min_F_r_i 3 1
## 92 peakCr_countor 1 1
## 93 peakCr_inside 1 1
## 94 peakVr_inside 2 1
## 95 SER_countor 3 1
## 96 SER_inside 3 1
## 97 skew_F_r_i 6 1
## 98 Slope_ini_countor 2 1
## 99 Slope_ini_inside 3 1
## 100 texture_contrast_nondir_post1 1 1
## 101 texture_contrast_nondir_post2 2 1
## 102 texture_contrast_nondir_post3 4 1
## 103 texture_correlation_nondir_post1 1 1
## 104 texture_correlation_nondir_post2 3 1
## 105 texture_correlation_nondir_post3 1 1
## 106 texture_correlation_nondir_post4 3 1
## 107 texture_diffentropy_nondir_post1 2 1
## 108 texture_diffentropy_nondir_post3 1 1
## 109 texture_diffentropy_nondir_post4 1 1
## 110 texture_diffvariance_nondir_post1 2 1
## 111 texture_diffvariance_nondir_post2 1 1
## 112 texture_diffvariance_nondir_post3 1 1
## 113 texture_diffvariance_nondir_post4 1 1
## 114 texture_energy_nondir_post2 1 1
## 115 texture_energy_nondir_post3 2 1
## 116 texture_energy_nondir_post4 3 1
## 117 texture_entropy_nondir_post1 1 1
## 118 texture_entropy_nondir_post4 1 1
## 119 texture_inversediffmoment_nondir_post1 1 1
## 120 texture_inversediffmoment_nondir_post2 3 1
## 121 texture_inversediffmoment_nondir_post3 3 1
## 122 texture_inversediffmoment_nondir_post4 5 1
## 123 texture_sumaverage_nondir_post1 1 1
## 124 texture_sumaverage_nondir_post2 2 1
## 125 texture_sumaverage_nondir_post3 3 1
## 126 texture_sumaverage_nondir_post4 2 1
## 127 texture_sumentropy_nondir_post2 1 1
## 128 texture_sumentropy_nondir_post4 1 1
## 129 texture_sumvariance_nondir_post1 5 1
## 130 texture_sumvariance_nondir_post2 1 1
## 131 texture_sumvariance_nondir_post3 1 1
## 132 texture_sumvariance_nondir_post4 4 1
## 133 texture_variance_nondir_post1 1 1
## 134 texture_variance_nondir_post2 1 1
## 135 texture_variance_nondir_post3 1 1
## 136 texture_variance_nondir_post4 1 1
## 137 Tpeak_countor 5 1
## 138 Tpeak_inside 1 1
## 139 UptakeRate_countor 1 1
## 140 UptakeRate_inside 2 1
## 141 V0 2 1
## 142 V1 1 1
## 143 V10 2 1
## 144 V11 1 1
## 145 V12 1 1
## 146 V13 2 1
## 147 V14 1 1
## 148 V15 1 1
## 149 V16 1 1
## 150 V18 3 1
## 151 V19 4 1
## 152 V2 7 1
## 153 V3 1 1
## 154 V4 3 1
## 155 V5 1 1
## 156 V6 3 1
## 157 V7 2 1
## 158 V8 3 1
## 159 V9 3 1
## 160 var_F_r_i 4 1
## 161 Vr_decreasingRate_countor 2 1
## 162 Vr_decreasingRate_inside 3 1
## 163 Vr_increasingRate_countor 2 1
## 164 Vr_increasingRate_inside 2 1
## 165 Vr_post_1_countor 2 1
## 166 Vr_post_1_inside 2 1
## 167 washoutRate_inside 1 1
#qplot(factor(selfeat), data=imgT1featsel, geom="bar", fill=factor(high))
ggplot(dfimgT1, aes(x=Var1, y=Freq, fill=factor(high))) +
geom_bar(stat = "identity") + coord_flip() +
ggtitle("imgT1featsel") +
labs(y="featsel frequency", x=" ") +
theme(plot.title = element_text(family = "Trebuchet MS", color="#666666", face="bold", size=22, hjust=0))+
theme(axis.title = element_text(family = "Trebuchet MS", color="#666666", face="bold", size=16))
## allfeatsel ###########
# pick frequency of 75% or higher as very common feature
dfall = data.frame(table(allfeatsel$selfeat))
dfall$high = (dfall$Freq>=0.5*max(allfeatsel$lop))*1
print(dfall[dfall$high==1, ])
## Var1 Freq high
## 1 A_countor 1 1
## 2 A_inside 10 1
## 3 alpha_countor 2 1
## 4 ave_T20 2 1
## 5 ave_T21 1 1
## 6 ave_T210 3 1
## 7 ave_T212 5 1
## 8 ave_T213 1 1
## 9 ave_T214 1 1
## 10 ave_T215 1 1
## 11 ave_T216 1 1
## 12 ave_T217 2 1
## 13 ave_T218 3 1
## 14 ave_T22 1 1
## 15 ave_T25 1 1
## 16 ave_T26 3 1
## 17 ave_T27 1 1
## 18 ave_T28 1 1
## 19 ave_T29 1 1
## 20 beta_inside 1 1
## 21 circularity 1 1
## 22 dce2SE0 1 1
## 23 dce2SE10 1 1
## 24 dce2SE13 2 1
## 25 dce2SE14 1 1
## 26 dce2SE15 1 1
## 27 dce2SE16 1 1
## 28 dce2SE17 1 1
## 29 dce2SE18 1 1
## 30 dce2SE19 1 1
## 31 dce2SE2 1 1
## 32 dce2SE3 1 1
## 33 dce2SE5 2 1
## 34 dce2SE6 1 1
## 35 dce2SE7 2 1
## 36 dce2SE8 1 1
## 37 dce3SE0 3 1
## 38 dce3SE1 2 1
## 39 dce3SE10 1 1
## 40 dce3SE11 3 1
## 41 dce3SE16 2 1
## 42 dce3SE17 2 1
## 43 dce3SE2 1 1
## 44 dce3SE3 1 1
## 45 dce3SE4 1 1
## 46 dce3SE6 2 1
## 47 dce3SE7 2 1
## 48 dce3SE9 1 1
## 49 earlySE0 1 1
## 50 earlySE10 1 1
## 51 earlySE11 1 1
## 52 earlySE14 2 1
## 53 earlySE17 1 1
## 54 earlySE18 2 1
## 55 earlySE19 4 1
## 56 earlySE2 2 1
## 57 earlySE3 3 1
## 58 earlySE4 1 1
## 59 earlySE5 1 1
## 60 earlySE6 1 1
## 61 earlySE8 1 1
## 62 earlySE9 1 1
## 63 edge_sharp_mean 3 1
## 64 edge_sharp_std 3 1
## 65 find_t2_signal_int 2 1
## 66 iiiMax_Margin_Gradient 1 1
## 67 iiMin_change_Variance_uptake 3 1
## 68 iMax_Variance_uptake 1 1
## 69 irregularity 4 1
## 70 ivVariance 4 1
## 71 k_Max_Margin_Grad 3 1
## 72 Kpeak_countor 3 1
## 73 Kpeak_inside 1 1
## 74 kurt_F_r_i 2 1
## 75 lateSE1 2 1
## 76 lateSE11 2 1
## 77 lateSE12 1 1
## 78 lateSE13 3 1
## 79 lateSE14 1 1
## 80 lateSE16 2 1
## 81 lateSE17 2 1
## 82 lateSE19 2 1
## 83 lateSE6 1 1
## 84 lateSE7 2 1
## 85 lateSE8 3 1
## 86 lateSE9 1 1
## 87 LMSIR 1 1
## 88 LMSIR_predicted 1 1
## 89 max_RGH_mean 1 1
## 90 max_RGH_var 3 1
## 91 max_RGH_var_k 1 1
## 92 maxCr_countor 2 1
## 93 maxCr_inside 1 1
## 94 maxVr_countor 1 1
## 95 maxVr_inside 1 1
## 96 mean_F_r_i 1 1
## 97 min_F_r_i 4 1
## 98 peakCr_inside 2 1
## 99 peakVr_countor 1 1
## 100 SER_countor 2 1
## 101 SER_inside 5 1
## 102 skew_F_r_i 2 1
## 103 T2_lesionSIstd 1 1
## 104 T2grad_margin 1 1
## 105 T2grad_margin_var 3 1
## 106 T2kurt_F_r_i 3 1
## 107 T2max_F_r_i 1 1
## 108 T2mean_F_r_i 1 1
## 109 T2min_F_r_i 1 1
## 110 T2RGH_mean 4 1
## 111 T2RGH_var 2 1
## 112 T2skew_F_r_i 2 1
## 113 T2texture_contrast_nondir 3 1
## 114 T2texture_correlation_nondir 2 1
## 115 T2texture_energy_nondir 3 1
## 116 T2texture_entropy_nondir 1 1
## 117 T2texture_inversediffmoment_nondir 2 1
## 118 T2texture_sumaverage_nondir 2 1
## 119 T2texture_sumentropy_nondir 1 1
## 120 T2texture_sumvariance_nondir 1 1
## 121 T2texture_variance_nondir 2 1
## 122 T2var_F_r_i 3 1
## 123 T2wSI_predicted 1 1
## 124 texture_contrast_nondir_post1 1 1
## 125 texture_contrast_nondir_post2 3 1
## 126 texture_correlation_nondir_post1 3 1
## 127 texture_correlation_nondir_post2 2 1
## 128 texture_correlation_nondir_post3 2 1
## 129 texture_diffentropy_nondir_post1 1 1
## 130 texture_diffentropy_nondir_post2 1 1
## 131 texture_diffentropy_nondir_post3 1 1
## 132 texture_diffentropy_nondir_post4 1 1
## 133 texture_diffvariance_nondir_post1 2 1
## 134 texture_diffvariance_nondir_post2 1 1
## 135 texture_diffvariance_nondir_post3 4 1
## 136 texture_energy_nondir_post1 3 1
## 137 texture_energy_nondir_post2 1 1
## 138 texture_energy_nondir_post3 1 1
## 139 texture_energy_nondir_post4 2 1
## 140 texture_entropy_nondir_post1 1 1
## 141 texture_entropy_nondir_post2 1 1
## 142 texture_entropy_nondir_post3 1 1
## 143 texture_entropy_nondir_post4 1 1
## 144 texture_inversediffmoment_nondir_post2 4 1
## 145 texture_inversediffmoment_nondir_post4 3 1
## 146 texture_sumaverage_nondir_post1 3 1
## 147 texture_sumaverage_nondir_post2 3 1
## 148 texture_sumaverage_nondir_post3 1 1
## 149 texture_sumaverage_nondir_post4 1 1
## 150 texture_sumentropy_nondir_post2 1 1
## 151 texture_sumentropy_nondir_post3 1 1
## 152 texture_sumentropy_nondir_post4 2 1
## 153 texture_sumvariance_nondir_post1 3 1
## 154 texture_sumvariance_nondir_post2 2 1
## 155 texture_sumvariance_nondir_post4 1 1
## 156 texture_variance_nondir_post1 3 1
## 157 texture_variance_nondir_post2 1 1
## 158 texture_variance_nondir_post3 1 1
## 159 Tpeak_countor 2 1
## 160 Tpeak_inside 1 1
## 161 UptakeRate_countor 2 1
## 162 UptakeRate_inside 2 1
## 163 V0 1 1
## 164 V10 4 1
## 165 V11 3 1
## 166 V12 4 1
## 167 V13 2 1
## 168 V14 3 1
## 169 V15 1 1
## 170 V16 2 1
## 171 V17 4 1
## 172 V18 1 1
## 173 V19 1 1
## 174 V2 1 1
## 175 V3 2 1
## 176 V4 2 1
## 177 V5 2 1
## 178 V6 3 1
## 179 V8 3 1
## 180 V9 1 1
## 181 var_F_r_i 5 1
## 182 Vr_decreasingRate_countor 2 1
## 183 Vr_decreasingRate_inside 4 1
## 184 Vr_increasingRate_countor 2 1
## 185 Vr_increasingRate_inside 1 1
## 186 Vr_post_1_countor 1 1
## 187 washoutRate_countor 1 1
## 188 washoutRate_inside 1 1
#qplot(factor(selfeat), data=allfeatsel, geom="bar", fill=factor(high))
ggplot(dfall, aes(x=Var1, y=Freq, fill=factor(high))) +
geom_bar(stat = "identity") + coord_flip() +
ggtitle("allfeatsel") +
labs(y="featsel frequency", x=" ") +
theme(plot.title = element_text(family = "Trebuchet MS", color="#666666", face="bold", size=22, hjust=0))+
theme(axis.title = element_text(family = "Trebuchet MS", color="#666666", face="bold", size=16))
###########
## plot ROCs each pass individually in l-o-p heldout test cases
par(mfrow=c(1,1))
n=15
colors = rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, alpha = 1)
# plot 1/4
p1 = calcAUC_plot(perf_imgT2$obs, perf_imgT2$C,
xptext=0.45, yptext=0.75 ,colors[2], atitle="")
## Area under the curve: 0.6689
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.4328689 0.5349 0.5967 0.6584 0.6328 0.6771 0.724
par(new=TRUE)
p2 = calcAUC_plot(perf_allT2$obs, perf_allT2$C,
xptext=0.55, yptext=0.65 ,colors[9], atitle="")
## Area under the curve: 0.6894
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3013366 0.7942 0.8395 0.8848 0.4398 0.4895 0.5393
par(new=TRUE)
p3 = calcAUC_plot(perf_imgT1$obs, perf_imgT1$C,
xptext=0.65, yptext=0.55 ,colors[11], atitle="")
## Area under the curve: 0.7544
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3756026 0.6296 0.6831 0.7407 0.6823 0.7266 0.7708
par(new=TRUE)
p4 = calcAUC_plot(perf_all$obs, perf_all$C,
xptext=0.75, yptext=0.45 ,colors[14], atitle="ROCs leave-one-patient out test ")
## Area under the curve: 0.7481
## 95% CI (2000 stratified bootstrap replicates):
## thresholds sp.low sp.median sp.high se.low se.median se.high
## 0.3979641 0.5432 0.6008 0.6626 0.7396 0.7839 0.8255
legend("bottomright",
legend = c(paste0("imgT2w"),
paste0("imgT2w+predT2w"),
paste0("imgT1w"),
paste0("imgT1+imgT2w+predT2w")),
col = c(colors[2],colors[9],colors[11],colors[14]), lwd = 2)
# find significants: only imgT2 vs. allT2
roc.test(p1$ROC, p2$ROC, method=c("bootstrap"), alternative = c("less"), boot.stratified=TRUE)
##
## Bootstrap test for two correlated ROC curves
##
## data: p1$ROC and p2$ROC
## D = -1.0023, boot.n = 2000, boot.stratified = 1, p-value = 0.1581
## alternative hypothesis: true difference in AUC is less than 0
## sample estimates:
## AUC of roc1 AUC of roc2
## 0.6687404 0.6893597
# find significants: mass imgT1 vs all
roc.test(p3$ROC, p4$ROC, method=c("bootstrap"), alternative = c("two.sided"), boot.stratified=TRUE)
##
## Bootstrap test for two correlated ROC curves
##
## data: p3$ROC and p4$ROC
## D = 0.34712, boot.n = 2000, boot.stratified = 1, p-value = 0.7285
## alternative hypothesis: true difference in AUC is not equal to 0
## sample estimates:
## AUC of roc1 AUC of roc2
## 0.7543885 0.7481031
# find significants: mass allT2 vs all
roc.test(p2$ROC, p4$ROC, method=c("bootstrap"), alternative = c("two.sided"), boot.stratified=TRUE)
##
## Bootstrap test for two correlated ROC curves
##
## data: p2$ROC and p4$ROC
## D = -2.2725, boot.n = 2000, boot.stratified = 1, p-value = 0.02305
## alternative hypothesis: true difference in AUC is not equal to 0
## sample estimates:
## AUC of roc1 AUC of roc2
## 0.6893597 0.7492082
### post training... to find out about a NH prediction in the test set
# library(nodeHarvest)
# kid = 10
# plot(treedata_all$forest, XTEST=T1T2test[kid,c(names(allfeatures[2:ncol(allfeatures)]))],
# highlight=1, labels="", cexfaclab=1)
#
# print(T1T2testinfo[kid,c(1,24:26)])
# predict(treedata_all$forest,
# newdata=T1T2test[kid,c(names(allfeatures[2:ncol(allfeatures)]))],
# explain=1, maxshow = 5)
